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1. Subproteomic signature comparison of in vitro selected fluoroquinolone resistance and ciprofloxacin stress in Salmonella Typhimurium DT104B

Author: Patrícia Poeta, Gilberto Igrejas, Carmen Torres, Manuela Caniça, Ingrid Chafsey, José Luis Capelo, Susana Correia, Christophe Chambon, Didier Viala, Michel Hébraud, department of neurology, clinical dementia center and DZNE, University Medical Centre Goettingen, Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), Qualité des Produits Animaux ( QUAPA ), Institut National de la Recherche Agronomique ( INRA ), Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Universidad de La Rioja ( UR ), National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR-HAI), Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, I.P, UCIBIO-REQUIMTE, Faculty of Science and Technology, Universidade Nova de Lisboa, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, Department of Genetics and Biotechnology, Department of Genetics and Biotechnology, Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (Portugal), Veterinary Science Department, Unidade de Ciencias Biomoleculares Aplicadas (UCIBIO), Requimte, Universidade do Porto [Porto]-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Área de Bioquímica y Biología Molecular, Universidad de La Rioja (UR), Faculty of Sciences and Technology (FCT NOVA), Universidade Nova de Lisboa (NOVA), Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto], Faculty of Sciences and Technology, ProteoMass Scientific Society, Universidade do Porto = University of Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto = University of Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Instituto Nacional de Saùde Dr Ricardo Jorge [Portugal] (INSA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Portuguese Foundation for Science and Technology (FCT) SFRH/BD/75160/2010, European Social Fund Ministry of Education and Science (MEC), national funds from FCT/MEC UID/Multi/04378/2013, ERDF under the PT Partnership Agreement POCI-01-0145-FEDER-007728, Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto, INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universidade do Porto-Departamento de Química (DQ), and Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: 0301 basic medicine, Salmonella, Proteome, [SDV]Life Sciences [q-bio], [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, education, Shotgun Proteomics, Salmonella Typhimurium DT104B, Biology, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, medicine.disease_cause, fluoroquinolone, Biochemistry, Microbiology, ciprofloxacine, 03 medical and health sciences, stress, Antibiotic resistance, Stress, Physiological, ciprofloxacin, Lc ms ms, Drug Resistance, Bacterial, medicine, antimicrobial resistance, Selection, Genetic, LC-MS/MS, Shotgun proteomics, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Comparative Subproteomics, [ SDV ] Life Sciences [q-bio], Resistência aos Antimicrobianos, comparative subproteomics, in vitro, 2-DE, salmonella Typhimurium DT104B, In vitro, Fluoroquinolone resistance, 3. Good health, Anti-Bacterial Agents, Ciprofloxacin, 030104 developmental biology, shotgun proteomics, Antimicrobial Resistance, salmonella typhimurium, medicine.drug, Fluoroquinolones
Abstract: Background: Fluoroquinolone resistance in nontyphoidal Salmonella is a situation of serious and international concern, particularly in S. Typhimurium DT104B multiresistant strains. Although known to be multifactorial, fluoroquinolone resistance is still far from a complete understanding. Methods: Subproteome changes between an experimentally selected fluoroquinolone-resistant strain (Se6-M) and its parent strain (Se6), and also in Se6-M under ciprofloxacin (CIP) stress, were evaluated in order to give new insights into the mechanisms involved. Proteomes were compared at the intracellular and membrane levels by a 2-DE~LC-MS/MS and a shotgun LC-MS/MS approach, respectively. Results: In total, 35 differentially abundant proteins were identified when comparing Se6 with Se6-M (25 more abundant in Se6 and 10 more abundant in Se6-M) and 82 were identified between Se6-M and Se6-M+CIP (51 more abundant in Se6-M and 31 more abundant under ciprofloxacin stress). Conclusion: Several proteins with known and possible roles in quinolone resistance were identified which provide important information about mechanism-related differential protein expression, supporting the current knowledge and also leading to new testable hypotheses on the mechanism of action of fluoroquinolone drugs. info:eu-repo/semantics/publishedVersion
Published: 2017

2. Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat

Author: Stéphanie Blanquet-Diot, Delphine Thevenot-Sergentet, Wessam Galia, Vincent Navratil, Cindy Garnier, Françoise Leriche, Audrey Dubost, Stéphane Cruveiller, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Unité Mixte de Recherche sur le Fromage - UMR 545 (UMRF), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Université Clermont Auvergne (UCA), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Pôle Rhône-Alpin de BioInformatique [Lyon] (PRABI), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Unité de Recherches Animal et Fonctionnalités des Produits Animaux ( URAFPA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lorraine ( UL ), Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), UR CALITYSS Consommateur, aliment, typique, sécurité, santé, Institut d'Enseignement Supérieur et de Recherche en Alimentation, Santé Animale, Sciences Agronomiques et de l'Environnement, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Institut des Sciences Analytiques ( ISA ), École normale supérieure - Lyon ( ENS Lyon ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique ( CNRS ), Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche sur le Fromage (UMRF), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche Fromagère ( UMRF ), Institut National de la Recherche Agronomique ( INRA ), Centre National de la Recherche Scientifique ( CNRS ), Laboratoire Bioinformatique Analyse Genome et Metabolisme, Université d'Evry Val d'Essonne, Rhone-Alpes Bioinformatics Center, Université Claude Bernard Lyon 1 ( UCBL ), Laboratoire Escherichia Coli, Unité Mixte de Recherche Fromagère - Clermont Auvergne ( UMRF ), Université Clermont Auvergne ( UCA ) -Institut national de la recherche agronomique [Auvergne/Rhône-Alpes] ( INRA Auvergne/Rhône-Alpes ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), and Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: 0301 basic medicine, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, [SDV]Life Sciences [q-bio], [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, medicine.disease_cause, 16S metagenomics analysis, Cell Wall, Gene expression, RNA-Seq, Amino Acids, natural microbiota, Pathogen, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Microbiota, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, ground beef, Enterohemorrhagic Escherichia coli, DNA microarray, escherichia coli, Research Article, Biotechnology, lcsh:QH426-470, lcsh:Biotechnology, 030106 microbiology, Down-Regulation, Virulence, Biology, Microbiology, 03 medical and health sciences, Species Specificity, microbiote, lcsh:TP248.13-248.65, Genetics, medicine, Gene, Escherichia coli, Nitrites, Nitrates, microorganisme, [ SDV ] Life Sciences [q-bio], Gene Expression Profiling, Cell Membrane, Biological Transport, Pathogenic bacteria, lcsh:Genetics, Red Meat, Metagenomics, EHEC, viande hachee, transcriptome, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition
Abstract: Background Enterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at levels greater than that of the pathogen E. coli. However, how the microbiota outcompetes the pathogenic bacteria is unknown. Our objective was to identify metabolic pathways of EHEC that were altered by natural microbiota in order to improve our understanding of the mechanisms controlling the growth and survival of EHECs in ground beef. Results Based on 16S metagenomics analysis, we identified the microbial community structure in our beef samples which was an essential preliminary for subtractively analyzing the gene expression of the EHEC strains. Then, we applied strand-specific RNA-seq to investigate the effects of this microbiota on the global gene expression of EHEC O2621765 and O157EDL933 strains by comparison with their behavior in beef meat without microbiota. In strain O2621765, the expression of genes connected with nitrate metabolism and nitrite detoxification, DNA repair, iron and nickel acquisition and carbohydrate metabolism, and numerous genes involved in amino acid metabolism were down-regulated. Further, the observed repression of ftsL and murF, involved respectively in building the cytokinetic ring apparatus and in synthesizing the cytoplasmic precursor of cell wall peptidoglycan, might help to explain the microbiota’s inhibitory effect on EHECs. For strain O157EDL933, the induced expression of the genes implicated in detoxification and the general stress response and the repressed expression of the peR gene, a gene negatively associated with the virulence phenotype, might be linked to the survival and virulence of O157:H7 in ground beef with microbiota. Conclusion In the present study, we show how RNA-Seq coupled with a 16S metagenomics analysis can be used to identify the effects of a complex microbial community on relevant functions of an individual microbe within it. These findings add to our understanding of the behavior of EHECs in ground beef. By measuring transcriptional responses of EHEC, we could identify putative targets which may be useful to develop new strategies to limit their shedding in ground meat thus reducing the risk of human illnesses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3957-2) contains supplementary material, which is available to authorized users.
Published: 2017

3. An antimicrobial peptide-resistant minor subpopulation of Photorhabdus luminescens is responsible for virulence

Author: Emeric Dubois, Sylvie Pagès, Anne Lanois, Julien Brillard, Maurine Bonabaud, Annabelle Mouammine, Sophie Gaudriault, Alain Givaudan, David Roche, Grégory Jubelin, Ludovic Legrand, Stéphane Cruveiller, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] ( DGIMI ), Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ), Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), Université Clermont Auvergne ( UCA ) -INRA Clermont-Ferrand-Theix, GenomiX, Institut de Génomique Fonctionnelle, Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de Génomique Fonctionnelle ( IGF ), Centre National de la Recherche Scientifique ( CNRS ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Montpellier 1 ( UM1 ) -Université de Montpellier ( UM ), Centre Interlangues - Texte, Image, Langage ( TIL ), Université de Bourgogne ( UB ), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Sécurité et Qualité des Produits d'Origine Végétale ( SQPOV ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Avignon et des Pays de Vaucluse ( UAPV ), Ecologie microbienne des insectes et interactions hôte-pathogène ( EMIP ), Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), INRA 2011_1333_03 2015_1333, Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Insecta, Operon, [SDV]Life Sciences [q-bio], [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, 030106 microbiology, Population, salmonella, Virulence, Drug resistance, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, peptide antimicrobien, Article, Bacterial genetics, Microbiology, 03 medical and health sciences, inhomogeneity, Disk Diffusion Antimicrobial Tests, Photorhabdus luminescens, Drug Resistance, Bacterial, Gene Order, hétérogénéité, Animals, education, ComputingMilieux_MISCELLANEOUS, photorhabdus luminescens, bactérie, education.field_of_study, Multidisciplinary, biology, Gene Expression Profiling, Enterobacteriaceae Infections, biology.organism_classification, bacterium, 030104 developmental biology, Regulon, Gene Expression Regulation, Genes, Bacterial, Mutation, Photorhabdus, Antimicrobial Cationic Peptides
Abstract: Some of the bacterial cells in isogenic populations behave differently from others. We describe here how a new type of phenotypic heterogeneity relating to resistance to cationic antimicrobial peptides (CAMPs) is determinant for the pathogenic infection process of the entomopathogenic bacterium Photorhabdus luminescens. We demonstrate that the resistant subpopulation, which accounts for only 0.5% of the wild-type population, causes septicemia in insects. Bacterial heterogeneity is driven by the PhoPQ two-component regulatory system and expression of pbgPE, an operon encoding proteins involved in lipopolysaccharide (LPS) modifications. We also report the characterization of a core regulon controlled by the DNA-binding PhoP protein, which governs virulence in P. luminescens. Comparative RNAseq analysis revealed an upregulation of marker genes for resistance, virulence and bacterial antagonism in the pre-existing resistant subpopulation, suggesting a greater ability to infect insect prey and to survive in cadavers. Finally, we suggest that the infection process of P. luminescens is based on a bet-hedging strategy to cope with the diverse environmental conditions experienced during the lifecycle.
Published: 2017
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4. GPR40 mediates potential positive effects of a saturated fatty acid enriched diet on bone

Author: Yohann Wittrant, François R Jornayvaz, Elisabeth Miot-Noirault, Fabien Wauquier, Gaël Y. Rochefort, Mohamed Asrih, Claire Philippe, Lauriane Bonnet, Annick Bernalier, Jean-François Landrier, Véronique Coxam, Jérémy Sadoine, ProdInra, Archive Ouverte, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Nutrition, obésité et risque thrombotique (NORT), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), UMR990, IMTV, Institut National de la Santé et de la Recherche Médicale (INSERM), Pathologies, Imagerie et Biothérapies oro-faciales (EA 2496), Université Paris Descartes - Paris 5 (UPD5), Service d'Endocrinologie, Diabétologie et Métabolisme, Centre Hospitalier Universitaire Vaudois [Lausanne] (CHUV), Microbiologie Environnement Digestif Santé (MEDIS), Physiopathologie des Adaptations Nutritionnelles (PhAN), Institut National de la Recherche Agronomique (INRA)-Université de Nantes (UN), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Physiopathologie de la Résorption Osseuse et Thérapie des Tumeurs Osseuses Primitives, Université de Nantes (UN)-Institut National de la Santé et de la Recherche Médicale (INSERM), Unité de Nutrition Humaine ( UNH ), Institut National de la Recherche Agronomique ( INRA ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Clermont Université, Nutrition, obésité et risque thrombotique ( NORT ), Institut National de la Recherche Agronomique ( INRA ) -Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Unité de Nutrition Humaine - Clermont Auvergne ( UNH ), Université Clermont Auvergne ( UCA ) -Institut national de la recherche agronomique [Auvergne/Rhône-Alpes] ( INRA Auvergne/Rhône-Alpes ), Institut National de la Santé et de la Recherche Médicale ( INSERM ), Pathologies, Imagerie et Biothérapies oro-faciales ( EA 2496 ), Université Paris Descartes - Paris 5 ( UPD5 ), Centre Hospitalier Universitaire Vaudois [Lausanne] ( CHUV ), Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), Université Clermont Auvergne ( UCA ) -INRA Clermont-Ferrand-Theix, Université de Nantes ( UN ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Aix Marseille Université ( AMU ) -Institut National de la Recherche Agronomique ( INRA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Nutriments Lipidiques et Prévention des Maladies Métaboliques, Université de la Méditerranée - Aix-Marseille 2-Institut National de la Recherche Agronomique ( INRA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ), Imagerie Moléculaire et Thérapie Vectorisée ( IMTV ), Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Cancéropôle CLARA-ITMO ' Technologies pour la Santé ', Microbiologie Equipe Qualité et Sécurité des Aliments ( INRA ), Institut National de la Recherche Agronomique ( INRA ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), and Université de Nantes (UN)-Université de Nantes (UN)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, Panniculitis, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Bone remodeling, Receptors, G-Protein-Coupled, 0302 clinical medicine, Bone Density, ComputingMilieux_MISCELLANEOUS, chemistry.chemical_classification, Bone mineral, GPR40, saturated fatty acid, Fatty Acids, medicine.anatomical_structure, high-fat diet, nutrition, Saturated fatty acid, Alimentation et Nutrition, Free fatty acid receptor, Female, free fatty acid receptor, aliment riche en graisse, Biotechnology, medicine.medical_specialty, endocrine system, Ovariectomy, Biology, Diet, High-Fat, ostéoporose, 03 medical and health sciences, Methylamines, Osteoclast, Internal medicine, Free fatty acid receptor 1, medicine, [SDV.MHEP.PHY]Life Sciences [q-bio]/Human health and pathology/Tissues and Organs [q-bio.TO], Animals, Food and Nutrition, [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, osteoporosis, Bone preservation, Osteopenia, RANK Ligand, Fatty acid, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Mice, Mutant Strains, Mice, Inbred C57BL, Disease Models, Animal, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, 030104 developmental biology, Endocrinology, chemistry, acide gras saturé, Propionates, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery, Food Science
Abstract: The authors would like to thank all the people who contributed to the ovariectomy procedures, the diet delivery, and the tissue sampling. They also thank Vincent Poitout and AMGEN for providing them the GPR40 mouse strain. They also express gratitude to Lisa Nucke for English grammar and syntax improvement; International audience; SCOPE: The stimulation of the free fatty acid receptor G-protein coupled receptor (GPR) 40 by GW9508 prevents bone loss by inhibiting osteoclast activity, both in vitro and in vivo. Here, we questioned whether the stimulation of the GPR40 receptor by dietary fatty acids may lead to the same beneficial effect on bone.METHODS AND RESULTS: We investigated (i) the impact of a fatty acid enriched diet (high-fat diet [HFD]) on bone health in C57/BL6 female mice depending on (ii) the estrogen status (ovariectomy) and (iii) the genotype (GPR40(+/+) or GPR40(-/-) ). Bone mineral density (BMD), body composition, weight, inflammation and bone remodeling parameters were monitored. HFD decreased BMD in HFD-SH-GPR40(+/+) mice but OVX failed to further impact BMD in HFD-OVX-GPR40(+/+) mice, while additional bone loss was observed in HFD-OVX-GPR40(-/-) animals. These data suggest that when stimulated by fatty acid enriched diets GPR40 contributes to counteract ovariectomy-induced bone alteration. The sparing effect is supported by the modulation of both the osteoprotegerin/receptor activator of nuclear factor kappa-B ligand (OPG/RANKL) ratio in blood stream and the expression level of inflammatory markers in adipose tissues. Bone preservation by GPR40 stimulation is dependent on the presence of long-chain saturated fatty acids.CONCLUSION: GPR40 contributes to counter ovariectomy-induced bone loss in a context of saturated fatty acid enrichment
Published: 2017

5. From pre- to postweaning: Transformation of the young calf's gastrointestinal tract

Author: H. Berends, S. J. Meale, Michael A. Steele, Le Luo Guan, Frédérique Chaucheyras-Durand, Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), Université Clermont Auvergne ( UCA ) -INRA Clermont-Ferrand-Theix, Lallemand Animal Nutrition, Trouw Nutrition R&D, Department of Agricultural Food and Nutrition Science, University of Alberta, Natural Science and Engineering Research Council (Ottawa, ON, Canada), Alberta Milk (Edmonton, AB, Canada), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), and Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Physiology, Weaning, Biology, 03 medical and health sciences, Nutrient flow, Rumen, lower gut, intestin, Genetics, Animals, calve, intestine, Barrier function, tractus gastrointestinal, 2. Zero hunger, Gastrointestinal tract, calf, rumen, [ SDV ] Life Sciences [q-bio], veau, 0402 animal and dairy science, forestomach, 04 agricultural and veterinary sciences, Animal Feed, 040201 dairy & animal science, Diet, Gastrointestinal Tract, Transformation (genetics), 030104 developmental biology, Animals, Newborn, Biochemistry, Dairy calf, Cattle, Animal Science and Zoology, Food Science, GIT diseases
Abstract: The ruminant gastrointestinal tract (GIT) faces the challenge of protecting the host from luminal contents and pathogens, while supporting the absorption and metabolism of nutrients for growth and maintenance. The GIT of the calf in early life undergoes some of the most rapid microbial and structural changes documented in nature, and these adaptations in GIT function make the young calf susceptible to GIT diseases and disorders. Despite these challenges, the calf's GIT has a certain degree of plasticity and can sense nutrient supply and respond to bioactive ingredients. Calf GIT research has historically focused on the transition during weaning and characterizing ruminal papillae development using microscopy and digesta metabolite responses. Through the use of new molecular-based approaches, we have recently shown that delaying the age of weaning and providing a step-down weaning protocol is associated with a more gradual shift in ruminal microbiota to a postweaned state. In addition to ruminal adaptations during weaning, nutrient flow to the lower gut changes dramatically during weaning, coinciding with a wide array of structural and microbiological changes. Structural and gene expression changes suggest that the lower gut of the dairy calf undergoes alterations that may reduce barrier function when solid feeds are consumed. More recently, in vivo data revealed that the weaning transition increases total gut permeability of the calf. Interestingly, the lower gut may be able to communicate with the forestomach, meaning that a nutrient can be sensed in the lower gut and cause subsequent adaptations in the forestomach. An improved understanding of how diet, microbiota, and functional ingredients interact to affect growth and barrier function of the intestinal tract would greatly benefit the dairy calf industry. A mechanistic understanding of such adaptations would also aid in the formulation of specific management regimens and provision of functional ingredients required to characterize and enhance gut function in young calves.
Published: 2017

6. Comparative subproteomic analysis of clinically acquired fluoroquinolone resistance and ciprofloxacin stress in Salmonella Typhimurium DT104B

Author: José Luis Capelo, Susana Correia, Christophe Chambon, Michel Hébraud, Yolanda Sáenz, Gilberto Igrejas, Didier Viala, Ingrid Chafsey, Patrícia Poeta, Functional Genomics and Proteomics Unit, Universidade de Trás-os-Montes e Alto Douro, Department of Genetics and Biotechnology, University of Tras-os-Montes and Alto Douro, Veterinary Science Department, University of Trás-os-Montes and Alto Douro (Portugal), Unidade de Ciencias Biomoleculares Aplicadas (UCIBIO), Requimte, Departamento de Química (DQ), Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Faculdade de Ciências e Tecnologia (FCT NOVA), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA)-Universidade do Porto [Porto], Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Faculty of Sciences and Technology (FCT NOVA), Universidade Nova de Lisboa (NOVA), Portuguese Foundation for Science and Technology (FCT) SFRH/BD/75160/2010, European Social Fund, Ministry of Education and Science (MEC), FCT/MEC UID/Multi/04378/2013, ERDF POCI-01-0145-FEDER-007728, Universidade do Porto = University of Porto-Departamento de Química (DQ), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto = University of Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), department of neurology, clinical dementia center and DZNE, University Medical Centre Goettingen, Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), Université Clermont Auvergne ( UCA ) -INRA Clermont-Ferrand-Theix, Qualité des Produits Animaux ( QUAPA ), Institut National de la Recherche Agronomique ( INRA ), Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Centro de Investigación Biomédica de La Rioja, UCIBIO-REQUIMTE, Faculty of Science and Technology, Universidade Nova de Lisboa, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, Universidade do Porto [Porto]-Departamento de Química (DQ), Universidade Nova de Lisboa (NOVA)-Universidade Nova de Lisboa (NOVA), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), Faculty of Sciences and Technology, Universidade Nova de Lisboa ( UNINOVA ), Universidade do Porto-Departamento de Química (DQ), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto-Departamento de Química (DQ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade do Porto, and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: 0301 basic medicine, Serotype, Salmonella, fluoroquinolone resistance, salmonella typhimurium DT104B, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, [SDV]Life Sciences [q-bio], Clinical Biochemistry, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, medicine.disease_cause, fluoroquinolone, Microbiology, ciprofloxacine, 03 medical and health sciences, Antibiotic resistance, Stress, Physiological, ciprofloxacin, Drug Resistance, Bacterial, medicine, Humans, antimicrobial resistance, ciprofloxacin stress, ComputingMilieux_MISCELLANEOUS, résistance antimicrobienne, biology, Strain (chemistry), [ SDV ] Life Sciences [q-bio], comparative subproteomics, biology.organism_classification, 3. Good health, Ciprofloxacin, 030104 developmental biology, Mechanism of action, Salmonella enterica, Proteome, medicine.symptom, salmonella typhimurium, medicine.drug
Abstract: PURPOSE Antimicrobial resistance is a worldwide public health threat and Salmonella enterica subsp. enterica serotype Typhimurium phage type DT104B multiresistant strains with additional quinolone resistance have been responsible for global outbreaks and high mortality. Quinolone resistance is known to be multifactorial but is still far from a complete understanding. To give new insights about the resistance mechanisms involved, this work aimed to evaluate subproteome changes between an S. Typhimurium DT104B clinical strain that acquired fluoroquinolone resistance after treatment (Se20) and its pretreatment parental strain (Se6), and also subproteome variations in Se20 under ciprofloxacin (CIP) stress (Se20+CIP). EXPERIMENTAL DESIGN The proteomes were compared at the intracellular and membrane levels by a 2-DE∼LC-MS/MS and a shotgun LC-MS/MS approach, respectively. RESULTS In total, 14 differentially abundant proteins were identified when comparing Se6 with Se20 and 91 were identified between Se20 and Se20+CIP. Several proteins with known and possible roles in quinolone resistance (AAC(6')-Ib-cr4, OmpD, OmpX, GlmS, GlmU, H-NS, etc.) were identified and discussed. CONCLUSIONS AND CLINICAL RELEVANCE The great number of proteins identified in this study provides important information about mechanism-related differential protein expression which supports the current knowledge and might lead to new testable hypotheses on the mechanism of action of fluoroquinolone drugs.
Published: 2017

7. Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes

Author: Belkorchia, Abdel, Pombert, Jean-François, Polonais, Valérie, Parisot, Nicolas, Delbac, Frédéric, Brugere, Jean François, Peyret, Pierre, Gaspin, Christine, Peyretaillade, Eric, Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne ( LMGE ), Université Clermont Auvergne ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique ( CNRS ), Department of Biology, Northern Arizona University [Flagstaff], Biologie Fonctionnelle, Insectes et Interactions ( BF2I ), Institut National de la Recherche Agronomique ( INRA ) -Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Université de Lyon-Institut National des Sciences Appliquées ( INSA ), EA 4678 CIDAM, Université Clermont Auvergne ( UCA ), Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), Unité de Mathématiques et Informatique Appliquées de Toulouse ( MIAT INRA ), Institut National de la Recherche Agronomique ( INRA ), National Institute of Allergy and Infectious Diseases of the National Institutes of Health [R15AI128627], Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Université Clermont Auvergne (UCA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: RNA, Untranslated, Base Sequence, Transcription, Genetic, [ SDV ] Life Sciences [q-bio], génomique comparative, [SDV]Life Sciences [q-bio], régulation transcriptionnelle, Encephalitozoon, eucaryote, Genomics, Full Papers, ncRNA structure, genome evolution, arn, microsporidia, ncRNA prediction, transcriptional regulation signals, Nosema, RNA, Small Nuclear, RNA, Small Nucleolar, Computer Simulation, Genome, Fungal
Abstract: Microsporidia are ubiquitous intracellular pathogens whose opportunistic nature led to their increased recognition with the rise of the AIDS pandemic. As the RNA world was largely unexplored in this parasitic lineage, we developed a dedicated in silico methodology to carry out exhaustive identification of ncRNAs across the Encephalitozoon and Nosema genera. Thus, the previously missing U1 small nuclear RNA (snRNA) and small nucleolar RNAs (snoRNAs) targeting only the LSU rRNA were highlighted and were further validated using 5' and 3'RACE-PCR experiments. Overall, the 15 ncRNAs that were found shared between Encephalitozoon and Nosema spp. may represent the minimal core set required for parasitic life. Interestingly, the systematic presence of a CCC- or GGG-like motif in 5' of all ncRNA and mRNA gene transcripts regardless of the RNA polymerase involved suggests that the RNA polymerase machineries in microsporidia species could use common factors. Our data provide additional insights in accordance with the simplification processes observed in these reduce genomes and underline the usefulness of sequencing closely related species to help identify highly divergent ncRNAs in these parasites.
Published: 2017

8. Transcriptomic adaptation of [i]staphylococcus xylosus[/i] to a cheese model

Author: Even, Sergine, Leroy, Sabine, Micheau, Pierre, De La Foye, Anne, Le Loir, Yves, Talon, Régine, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Unité de Microbiologie (MIC), Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Science et Technologie du Lait et de l'Oeuf ( STLO ), Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), Université Clermont Auvergne ( UCA ) -INRA Clermont-Ferrand-Theix, Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Microbiologie Environnement Digestif Santé (MEDIS), and INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, transcriptomique, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [ SDV.IDA ] Life Sciences [q-bio]/Food engineering, fromage, staphylococcus xylosus, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, produit laitier
Abstract: Staphylococcus xylosus belongs to the food-related species of coagulase-negative staphylococci. Thisspecies is present in the natural microbiota of traditional cheeses. It is also commercially available as an adjunct culture to enhance the aroma and texture of cheeses, as well as the color of the surface of smeared cheeses. The molecular mechanisms allowing the growth and adaptation of S. xylosus in the dairy products are still poorly understood. A microarray representing the S. xylosus C2a genome was used to determine how the gene expression profile was modified during growth and adaptation to a cheese model. The C2a strain was inoculated at 5.6 log CFU/g in ultra filtered milk concentrated 5.5-fold and supplemented with UHT cream and salt. Then rennet was added. The temperature of incubation was decreased from 30°C to 12°C after 10 hours of culture, to mimic the temperature shift generally encountered during cheese making. The growth of S. xylosus in the cheese model was exponential until 5 hours and reached a maximum of 8.7 log CFU/g at 24h. S. xylosus population remained almost at this population level after 48 hours of incubation. Total RNA extractions were performed directly from the solid dairy matrix inoculated with S. xylosus after 6, 24 and 48 hours of incubation. Compared to the 6 hours time point sampling, more than 1000 genes of S. xylosuswere differentially expressed at 24 and/or 48 hours of incubation. In particular, extensive upregulation of genes involved in the biosynthesis of purines, pyrimidines, aromatic amino acids and arginine was observed.This work generates a comprehensive genome-wide picture of what genes are modulated during S. xylosus growth and adaptation to a cheese model. Our study increases the understanding of the physiology of adjunct culture in the first step of cheese making process.
Published: 2016

9. Exploring the diversity of listeria monocytogenes biofilm architecture by high-throughput confocal laser scanning microscopy and the predominance of the honeycomb-like morphotype

Author: Morgan Guilbaud, Sylvain Brisse, Pascal Piveteau, Romain Briandet, Mickaël Desvaux, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Microbiologie Equipe Qualité et Sécurité des Aliments (INRA), Institut National de la Recherche Agronomique (INRA), Unité de Microbiologie (MIC), Génomique évolutive des Microbes / Microbial Evolutionary Genomics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique funding, SECurité des ALIments et Microbiologie, Institut National de la Recherche Agronomique (INRA)-École nationale d'ingénieurs des techniques des industries agricoles et alimentaires (ENITIAA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Guilbaud, Morgan, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), MICrobiologie de l'ALImentation au Service de la Santé humaine ( MICALIS ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), Génomique évolutive des Microbes, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Microbiologie Environnement Digestif Santé (MEDIS), and INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], chaîne alimentaire, strain origin, microscopie confocale à balayage laser, medicine.disease_cause, Applied Microbiology and Biotechnology, biofilm, chemistry.chemical_compound, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, Pathogen, morphotype, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Growth medium, Microscopy, Confocal, Ecology, Microbiology and Parasitology, descripteur, Microbiologie et Parasitologie, environnement, phénotype, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, motility, analyse quantitative, optimization, Biotechnology, agent pathogène, Pseudomonas-aeruginosa biofilm, pathogen, lineage, growth-condition, extracellular DNA, quantification, hydrophobicity, Biotechnologies, Biology, Honeycomb like, Microbiology, 03 medical and health sciences, Listeria monocytogenes, Confocal laser scanning microscopy, medicine, Crystal violet, 030304 developmental biology, diversité, 030306 microbiology, Biofilm, [ SDV.BIO ] Life Sciences [q-bio]/Biotechnology, biochemical phenomena, metabolism, and nutrition, Extracellular dna, High-Throughput Screening Assays, chemistry, Biofilms, Food Microbiology, Microbial Interactions, listeria monocytogènes, Food Science
Abstract: Listeria monocytogenes is involved in food-borne illness with a high mortality rate. The persistence of the pathogen along the food chain can be associated with its ability to form biofilms on inert surfaces. While most of the phenotypes associated with biofilms are related to their spatial organization, most published data comparing biofilm formation by L. monocytogenes isolates are based on the quantitative crystal violet assay, which does not give access to structural information. Using a high-throughput confocal-imaging approach, the aim of this work was to decipher the structural diversity of biofilms formed by 96 L. monocytogenes strains isolated from various environments. Prior to large-scale analysis, an experimental design was created to improve L. monocytogenes biofilm formation in microscopic-grade microplates, with special emphasis on the growth medium composition. Microscopic analysis of biofilms formed under the selected conditions by the 96 isolates revealed only weak correlation between the genetic lineages of the isolates and the structural properties of the biofilms. However, a gradient in their geometric descriptors (biovolume, mean thickness, and roughness), ranging from flat multilayers to complex honeycomb-like structures, was shown. The dominant honeycomb-like morphotype was characterized by hollow voids hosting free-swimming cells and localized pockets containing mixtures of dead cells and extracellular DNA (eDNA).
Published: 2015

10. Colonization of the meat extracellular matrix proteins by O157 and non-O157 enterohemorrhagic Escherichia coli

Author: Mickaël Desvaux, Estelle Loukiadis, S. Ganet, Nelly Caccia, Yolande Bertin, Thierry Astruc, Caroline Chagnot, Alexandra Durand, Régine Talon, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Laboratory, National Reference Laboratory for E. coli, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), MICrobiologie de l'ALImentation au Service de la Santé humaine ( MICALIS ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), Université Clermont Auvergne ( UCA ) -INRA Clermont-Ferrand-Theix, Université Claude Bernard Lyon 1 ( UCBL ), Ecologie microbienne ( EM ), Centre National de la Recherche Scientifique ( CNRS ) -Ecole Nationale Vétérinaire de Lyon ( ENVL ) -Université Claude Bernard Lyon 1 ( UCBL ), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique ( INRA ) -VetAgro Sup ( VAS ), Qualité des Produits Animaux ( QUAPA ), Institut National de la Recherche Agronomique ( INRA ), Unité de Microbiologie (MIC), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Microbiologie Environnement Digestif Santé (MEDIS), and INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: Serotype, Meat, meat contamination, Virulence Factors, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, Bacterial Toxins, Biology, medicine.disease_cause, Escherichia coli O157, shiga-toxin producing E. coli, Microbiology, Non o157, Extracellular matrix, Human health, [ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology, medicine, media_common.cataloged_instance, Animals, Humans, Colonization, European union, Escherichia coli, media_common, 2. Zero hunger, Extracellular Matrix Proteins, Escherichia coli Proteins, Biofilm, extracellular matrix protein, General Medicine, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, bacterial adhesion, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biofilms, Food Microbiology, biofilm formation, bacteria, Cattle, enterohemorrhagic escherichia coli, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science
Abstract: Enterohemorrhagic Escherichia coli (EHEC) are anthropozoonotic agents that range third among food-borne pathogens respective to their incidence and dangerousness in the European Union. EHEC are Shiga-toxin producing E. coli (STEC) responsible for foodborne poisoning mainly incriminated to the consumption of contaminated beef meat. Among the hundreds of STEC serotypes identified, EHEC mainly belong to O157:H7 but non-O157 can represent 20 to 70% of EHEC infections per year. Seven of those serogroups are especially of high-risk for human health, i.e. O26, O45, O103, O111, O121, O145 and O104. While meat can be contaminated all along the food processing chain, EHEC contamination essentially occurs at the dehiding stage of slaughtering. Investigating bacterial colonization to the skeletal-muscle extracellular matrix (ECM) proteins, it appeared that environmental factors influenced specific and non-specific bacterial adhesion of O157 and non-O157 EHEC as well as biofilm formation. Importantly, mechanical treatment (i.e. shaking, centrifugation, pipetting and vortexing) inhibited and biased the results of bacterial adhesion assay. Besides stressing the importance of the protocol to investigate bacterial adhesion to ECM proteins, this study demonstrated that the colonization abilities to ECM proteins vary among EHEC serogroups and should ultimately be taken into consideration to evaluate the risk of contamination for different types of food matrices.
Published: 2014

11. The Gluconeogenesis Pathway Is Involved in Maintenance of Enterohaemorrhagic Escherichia coli O157:H7 in Bovine Intestinal Content

Author: Victor P. J. Gannon, Evelyne Forano, Anne de la Foye, Christiane Deval, Yolande Bertin, Christine Martin, Josée Harel, Luke Masson, Mickaël Desvaux, Unité de Microbiologie (MIC), Institut National de la Recherche Agronomique (INRA), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), National Research Council of Canada (NRC), Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Groupe de Recherche sur les Maladies Infectieuses du Porc, Faculté de Médecine Vétérinaire, Université de Montréal (UdeM), Food-CT-2006-32241, Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Université de Montréal, VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), Université Clermont Auvergne ( UCA ) -INRA Clermont-Ferrand-Theix, Unité de Nutrition Humaine ( UNH ), Clermont Université-Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Institut National de la Recherche Agronomique ( INRA ), Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), and National Research Council of Canada ( NRC )
Subjects: bovin, voie métabolique, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, phosphoenolpyruvate carboxykinase (GTP), complementary DNA, intestin grêle, Polymerase Chain Reaction, nitrogen, Serine, chemistry.chemical_compound, enterohemorrhagic Escherichia coli, Microbial Physiology, chemistry.chemical_classification, Escherichia Coli, Multidisciplinary, glycerophosphate, asparagine, unclassified drug, Amino acid, Bacterial Pathogens, Intestines, dicarboxylic acid, Biochemistry, Medical Microbiology, Alimentation et Nutrition, Medicine, wild type, phosphoenolpyruvate, Agmatine, Phosphoenolpyruvate carboxykinase, amino acid, Research Article, ethanolamine, Science, glycerol, urea, Biology, Escherichia coli O157, Microbiology, serine, e coli 0157 h7, Glycerol, Food and Nutrition, Animals, tryptophan, analyse du transcriptome, agmatine, Microbial Pathogens, gluconeogénèse, DNA Primers, Base Sequence, lactic acid, DNA microarray, Gluconeogenesis, Biology and Life Sciences, nucleotide sequence, bacterial strain, biology.organism_classification, threonine, RNA extraction, Metabolic pathway, pyruvate water dikinase, chemistry, aspartic acid, carbon source, gene expression, Cattle, gastrointestinal tract, transcriptome, small intestine, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, upregulation, Bacteria, glycine, tricarboxylic acid
Abstract: Enterohaemorrhagic Escherichia coli (EHEC) are responsible for outbreaks of food- and water-borne illness. The bovine gastrointestinal tract (GIT) is thought to be the principle reservoir of EHEC. Knowledge of the nutrients essential for EHEC growth and survival in the bovine intestine may help in developing strategies to limit their shedding in bovine faeces thus reducing the risk of human illnesses. To identify specific metabolic pathways induced in the animal GIT, the transcriptome profiles of EHEC O157:H7 EDL933 during incubation in bovine small intestine contents (BSIC) and minimal medium supplemented with glucose were compared. The transcriptome analysis revealed that genes responsible for the assimilation of ethanolamine, urea, agmatine and amino acids (Asp, Thr, Gly, Ser and Trp) were strongly up-regulated suggesting that these compounds are the main nitrogen sources for EHEC in BSIC. A central role for the gluconeogenesis pathway and assimilation of gluconeogenic substrates was also pinpointed in EHEC incubated in BSIC. Our results suggested that three amino acids (Asp, Ser and Trp), glycerol, glycerol 3-phosphate, L-lactate and C4-dicarboxylates are important carbon sources for EHEC in BSIC. The ability to use gluconeogenic substrates as nitrogen sources (amino acids) and/or carbon sources (amino acids, glycerol and lactate) may provide a growth advantage to the bacteria in intestinal fluids. Accordingly, aspartate (2.4 mM), serine (1.9 mM), glycerol (5.8 mM) and lactate (3.6 mM) were present in BSIC and may represent the main gluconeogenic substrates potentially used by EHEC. A double mutant of E. coli EDL933 defective for phosphoenolpyruvate synthase (PpsA) and phosphoenolpyruvate carboxykinase (PckA), unable to utilize tricarboxylic acid (TCA) intermediates was constructed. Growth competition experiments between EHEC EDL933 and the isogenic mutant strain in BSIC clearly showed a significant competitive growth advantage of the wild-type strain further illustrating the importance of the gluconeogenesis pathway in maintaining EHEC in the bovine GIT. © 2014 Bertin et al.
Published: 2014

12. Draft Genome Sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium, Three Species with Equivocal Pathogenic Status for Cattle

Author: Alain Blanchard, Lucia Manso-Silvan, Emilie Dordet-Frisoni, Daniel J. Jacob, François Poumarat, Christine Citti, Laurent-Xavier Nouvel, Pascal Sirand-Pugnet, Claire Lemaitre, Patricia Thebault, Aurélien Barré, Macha Nikolski, Patrice Gaurivaud, Marc Breton, François Thiaucourt, Sébastien Theil, Florence Tardy, Virginie Dupuy, Carole Couture, Eric Baranowski, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire de Lyon [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Génétique Cellulaire (LGC), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Université Bordeaux Segalen - Bordeaux 2, Institut de recherche en astrophysique et planétologie (IRAP), Institut national des sciences de l'Univers (INSU - CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Ecole Nationale Vétérinaire de Toulouse (ENVT), Unité de Microbiologie (MIC), Institut National de la Recherche Agronomique (INRA), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Mycoplasmoses des Ruminants - UMR (MYCO), Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-CentraleSupélec-Télécom Bretagne-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Génomique, développement et pouvoir pathogène (GD2P), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Université de Bordeaux (UB)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Centre National de la Recherche Scientifique (CNRS), Financial support was provided by the EVOLMYCO project (ANR-07-GMGE-0001) from ANR to Alain Blanchard (Principal Investigator [PI]), François Thiaucourt (Co-PI), François Poumarat (Co-PI), and Christine Citti (Co-PI)., ANR-07-GMGE-0001,EVOLMYCO,Etude à grande échelle des génomes des mycoplasmes de ruminants : évolution et adaptation de bactéries minimales à des hôtes complexes(2007), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Lyon, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec, Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Contrôle des maladies animales exotiques et émergentes [Montpellier] ( CMAEE ), Institut National de la Recherche Agronomique ( INRA ) -Centre de coopération internationale en recherche agronomique pour le développement [CIRAD] : UMR15, ANSES, Laboratoire de Génétique Cellulaire ( LGC ), Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Vétérinaire de Toulouse, Interactions hôtes-agents pathogènes [Toulouse] ( IHAP ), Institut de recherche en astrophysique et planétologie ( IRAP ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Observatoire Midi-Pyrénées ( OMP ) -Centre National de la Recherche Scientifique ( CNRS ), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 ( UGSF ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Biologie du fruit et pathologie ( BFP ), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA ) -Université Sciences et Technologies - Bordeaux 1, Ecole Nationale Vétérinaire de Toulouse, Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), INRA - Mathématiques et Informatique Appliquées ( Unité MIAJ ), Institut National de la Recherche Agronomique ( INRA ), Mycoplasmoses des ruminants [Lyon], Université de Lyon-VetAgro Sup ( VAS ), VetAgro Sup ( VAS ), Centre de Bioinformatique de Bordeaux ( CBIB ), Scalable, Optimized and Parallel Algorithms for Genomics ( GenScale ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -GESTION DES DONNÉES ET DE LA CONNAISSANCE ( IRISA-D7 ), Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), CentraleSupélec-Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ) -CentraleSupélec-Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ) -Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ), Laboratoire Bordelais de Recherche en Informatique ( LaBRI ), Centre National de la Recherche Scientifique ( CNRS ) -École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Laboratoire Microorganismes : Génome et Environnement ( LMGE ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Centre National de la Recherche Scientifique ( CNRS ), Génomique, développement et pouvoir pathogène ( GD2P ), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA )
Subjects: 0303 health sciences, 030306 microbiology, Biology, Mycoplasma arginini, L73 - Maladies des animaux, Genome, Virology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Microbiology, 03 medical and health sciences, [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Genetics, Prokaryotes, Mycoplasma bovigenitalium, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Molecular Biology, health care economics and organizations, 030304 developmental biology, Mycoplasma alkalescens
Abstract: We report here the draft genome sequences of Mycoplasma alkalescens , Mycoplasma arginini , and Mycoplasma bovigenitalium . These three species are regularly isolated from bovine clinical specimens, although their role in disease is unclear.
Published: 2013

13. Complete Genome Sequence of Mycoplasma putrefaciens Strain 9231, One of the Agents of Contagious Agalactia in Goats

Author: Aurélien Barré, Alain Blanchard, Florence Tardy, Pascal Sirand-Pugnet, Daniel J. Jacob, Lucia Manso-Silvan, Christine Citti, Emilie Dordet-Frisoni, Patricia Thebault, Sébastien Theil, Patrice Gaurivaud, François Thiaucourt, Virginie Dupuy, Laurent-Xavier Nouvel, Carole Couture, François Poumarat, Macha Nikolski, Eric Baranowski, Claire Lemaitre, Marc Breton, INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), Génomique, développement et pouvoir pathogène (GD2P), Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Bordeaux Segalen - Bordeaux 2, Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 (UGSF), Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Mycoplasmoses des Ruminants - UMR (MYCO), Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre de Bioinformatique de Bordeaux (CBIB), CGFB, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UNIV-RENNES)-CentraleSupélec-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Université de Bretagne Sud (UBS)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Rennes (ENS Rennes)-Télécom Bretagne-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec, Contrôle des maladies animales exotiques et émergentes (UMR CMAEE), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Laboratoire de Lyon, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Institut de recherche en astrophysique et planétologie (IRAP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Unité de Glycobiologie Structurale et Fonctionnelle UMR 8576 (UGSF), Institut National de la Recherche Agronomique (INRA)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Unité de Microbiologie (MIC), GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-Télécom Bretagne-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Lyon [ANSES], Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS), INRA - Mathématiques et Informatique Appliquées ( Unité MIAJ ), Institut National de la Recherche Agronomique ( INRA ), Génomique, développement et pouvoir pathogène ( GD2P ), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA ), Laboratoire de Génétique Cellulaire ( LGC ), Institut National de la Recherche Agronomique ( INRA ) -Ecole Nationale Vétérinaire de Toulouse, Interactions hôtes-agents pathogènes [Toulouse] ( IHAP ), Unité de Glycobiologie Structurale et Fonctionnelle - UMR 8576 ( UGSF ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lille-Centre National de la Recherche Scientifique ( CNRS ), Biologie du fruit et pathologie ( BFP ), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA ) -Université Sciences et Technologies - Bordeaux 1, Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), Mycoplasmoses des ruminants [Lyon], Université de Lyon-VetAgro Sup ( VAS ), VetAgro Sup ( VAS ), Centre de Bioinformatique de Bordeaux ( CBIB ), Scalable, Optimized and Parallel Algorithms for Genomics ( GenScale ), Institut National de Recherche en Informatique et en Automatique ( Inria ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -GESTION DES DONNÉES ET DE LA CONNAISSANCE ( IRISA-D7 ), Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), CentraleSupélec-Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ) -CentraleSupélec-Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -Institut National de Recherche en Informatique et en Automatique ( Inria ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ) -Institut de Recherche en Informatique et Systèmes Aléatoires ( IRISA ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -Télécom Bretagne-Institut National des Sciences Appliquées ( INSA ) -École normale supérieure - Rennes ( ENS Rennes ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Bretagne Sud ( UBS ), Contrôle des maladies animales exotiques et émergentes [Montpellier] ( CMAEE ), Institut National de la Recherche Agronomique ( INRA ) -Centre de coopération internationale en recherche agronomique pour le développement [CIRAD] : UMR15, Laboratoire Bordelais de Recherche en Informatique ( LaBRI ), Centre National de la Recherche Scientifique ( CNRS ) -École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, ANSES, Laboratoire Microorganismes : Génome et Environnement ( LMGE ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Centre National de la Recherche Scientifique ( CNRS ), Ecole Nationale Vétérinaire de Toulouse, Institut de recherche en astrophysique et planétologie ( IRAP ), Université Paul Sabatier - Toulouse 3 ( UPS ) -Observatoire Midi-Pyrénées ( OMP ) -Centre National de la Recherche Scientifique ( CNRS ), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), The annotation of the genome was performed within the EVOLMYCO project, financed by the French national agency for research (ANR-07-GMGE-001)., and ANR-07-GMGE-0001,EVOLMYCO,Etude à grande échelle des génomes des mycoplasmes de ruminants : évolution et adaptation de bactéries minimales à des hôtes complexes(2007)
Subjects: Whole genome sequencing, Genetics, 0303 health sciences, 030306 microbiology, Strain (biology), education, Biology, L73 - Maladies des animaux, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, Microbiology, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM], Mycoplasma putrefaciens, Prokaryotes, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Molecular Biology, 030304 developmental biology
Abstract: Mycoplasma putrefaciens is one of the etiologic agents of contagious agalactia in goats. We report herein the complete genome sequence of Mycoplasma putrefaciens strain 9231.
Published: 2013

14. Correction: Benefits of the ipowder® extraction process applied to Melissa officinalis L.: improvement of antioxidant activity and in vitro gastro-intestinal release profile of rosmarinic acid

Author: Valérie Bardot, Anaïs Escalon, Isabelle Ripoche, Sylvain Denis, Monique Alric, Sandrine Chalancon, Pierre Chalard, César Cotte, Lucile Berthomier, Martin Leremboure, Michel Dubourdeaux, PiLeJe Industrie, SIGMA Clermont (SIGMA Clermont), Microbiologie Environnement Digestif Santé (MEDIS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Chimie de Clermont-Ferrand (ICCF), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Sigma CLERMONT (Sigma CLERMONT)-Centre National de la Recherche Scientifique (CNRS), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Institut de Chimie de Clermont-Ferrand - Clermont Auvergne (ICCF), Sigma CLERMONT (Sigma CLERMONT)-Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Sigma CLERMONT (Sigma CLERMONT)
Subjects: 0303 health sciences, 03 medical and health sciences, 030309 nutrition & dietetics, activité antioxydante, feuille seche, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, General Medicine, tractus gastro-intestinal, acide rosmarinique, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Food Science
Abstract: International audience; The objective of this study was to evaluate the benefits of a new extraction process, the ipowder (R) technology, applied to Melissa officinalis L. Compared to M. officinalis ground dry leaves, the ipowder (R) had a similar phytochemical fingerprint but contained twice the concentration of rosmarinic acid (by HPTLC and HPLC) and had a two-fold greater antioxidant activity (DPPH* method). In vitro digestion experiments (TIM-1 model) showed better availability of rosmarinic acid for intestinal absorption with the ipowder (R) than with ground dry leaves, manifested by a three-fold reduction in the quantity of ingested product needed for delivery of the same amount of rosmarinic acid into the upper gastro-intestinal tract. This study shows that the ipowder (R) technology preserves all the original plant compounds intact while making some active ingredients more accessible and available to exert their effects. To obtain a given effect, the amount of ipowder (R) extract to ingest will therefore be lower; a reduction in the daily dosage will be more convenient for the patient and will improve patient compliance with supplementation.
Published: 2020

15. Effect of procyanidin on dietary iron absorption in hereditary hemochromatosis and in dysmetabolic iron overload syndrome: A crossover double-blind randomized controlled trial

Author: Jean-Michel Cardot, Hervé Lobbes, Marc Ruivard, Christian Dualé, Bruno Pereira, Andrzej Mazur, Cécile Gladine, CHU Clermont-Ferrand, Unité de Nutrition Humaine (UNH), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Chimie Radicalaire (ICR), Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), CHU Gabriel Montpied [Clermont-Ferrand], CIC Clermont Ferrand, Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand-CHU Clermont-Ferrand-Centre de Pharmacologie Clinique, Neuro-Dol (Neuro-Dol), Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Microbiologie Environnement Digestif Santé (MEDIS), CHU Estaing [Clermont-Ferrand], Clermont-Ferrand University Hospital, Médecine interne, Centre Hospitalier Régional Universitaire de Tours (CHRU Tours), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Biostatistiques, Inferential, CIC 1405, CIC/Centre de Pharmacologie Clinique, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Clermont-Ferrand, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, SIGMA Clermont, Université Clermont Auvergne (UCA), Centre National de la Recherche Scientifique (CNRS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Université Clermont Auvergne (UCA)-Institut National de la Recherche Agronomique (INRA), Clermont Université-Université d'Auvergne - Clermont-Ferrand I (UdA)-Institut National de la Recherche Agronomique (INRA), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), CHU Gabriel Montpied (CHU), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Pharmacologie Clinique-CHU Gabriel-Montpied, and CCSD, Accord Elsevier
Subjects: 0301 basic medicine, Male, Polyphenol supplementation, Critical Care and Intensive Care Medicine, Gastroenterology, Antioxidants, Catechin, law.invention, 0302 clinical medicine, Randomized controlled trial, law, Medicine, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, Meal, Nutrition and Dietetics, Cross-Over Studies, medicine.diagnostic_test, Area under the curve, Middle Aged, 3. Good health, Iron absorption, [SDV.SP.PHARMA] Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, Hereditary hemochromatosis, Serum iron, Female, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Hemochromatosis, Iron, Dietary, medicine.medical_specialty, [SDV.SP.MED] Life Sciences [q-bio]/Pharmaceutical sciences/Medication, Iron Overload, 030209 endocrinology & metabolism, Placebo, Type I hereditary hemochromatosis, 03 medical and health sciences, Dysmetabolic iron-overload syndrome, Double-Blind Method, [SDV.SP.MED]Life Sciences [q-bio]/Pharmaceutical sciences/Medication, Internal medicine, Biflavonoids, Humans, Proanthocyanidins, [SDV.NEU] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], 030109 nutrition & dietetics, business.industry, Iron-overload diseases, Bioavailability, Basal (medicine), [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology, business, ron absorption, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Procyanidin
Abstract: International audience; Background & aims: Type I hereditary hemochromatosis (HH) and dysmetabolic iron overload syndrome (DIOS) are the two most prevalent iron overload diseases. Although many food components, particularly polyphenols, reduce iron bioavailability, there is no clinically validated nutritional strategy to reduce food-iron absorption in patients with these diseases. We aimed to determine whether supplementation with 100 mg of procyanidins during a meal reduces dietary iron absorption in patients with HH or DIOS.Methods: 20 HH and 20 DIOS patients were enrolled in a double-blind three-period crossover randomized study. Basal serum iron level was measured following an overnight fast. Each patient consumed a standardized test iron-rich meal containing 43 mg of iron with two capsules of placebo or procyanidin supplementation. Each period was separated by a 3-day wash-out period. The primary objective was a reduction of dietary iron absorption, assessed by a reduction of serum-iron area under the curve (AUC) corrected for baseline serum iron.Results: All patients completed the study. The meal and the procyanidin supplements were well tolerated. In both HH and DIOS patients, the iron-rich meal induced a significant increase of serum iron compared with baseline at 120, 180, 240 min, from 8 to 9.1%(p = 0.002, 0.001 and 0.003, respectively) in DIOS and from 15.8 to 25.7% (p < 0.001) in HH. Iron absorption was 3.5-fold higher in HH than in DIOS (p < 0.001). Procyanidin supplementation did not significantly modify iron absorption in DIOS (AUC of added iron 332.87 +/- 649.55 vs 312.61 +/- 678.61 mu mol.h/L, p = 0.916) or in HH (1168.62 +/- 652.87 vs 1148.54 mu mol.h/L +/- 1290.05, p = 0.917).Conclusions: An iron-rich test meal led to a marked increase in iron absorption in HH but a mild increase in DIOS. Procyanidin supplementation does not significantly reduce dietary iron absorption in either disease. (C) 2019 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism.
Published: 2020

16. Putative Protein Biomarkers of Escherichia coli Antibiotic Multiresistance Identified by MALDI Mass Spectrometry

Author: Bardot, Valérie, Escalon, Anaïs, Ripoche, Isabelle, Denis, Sylvain, ALRIC, Monique, Chalancon, Sandrine, Chalard, Pierre, Cotte, César, Berthomier, Lucile, Leremboure, Martin, Dubourdeaux, Michel, Universidade de Trás-os-Montes e Alto Douro (UTAD), Universidade do Trás-os-Montes e Alto Douro, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Qualité des Produits Animaux (QuaPA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Microbiologie Environnement Digestif Santé (MEDIS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 'Espectrometria de massa e sequenciacao aplicadas a microbiologia clinica moderna: pesquisa e identificacao de biomarcadores em especies bacterianas multiresistentes' (Programa de Accoes Universitarias Integradas Luso-Francesas) TC-14/2017Associate Laboratory for Green Chemistry-LAQV - FCT/MCTES UIDB/50006/2020, VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), Tissus animaux, nutrition, digestion, écosystème et métabolisme (TANDEM), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-INP. Ecole Nationale Supérieure Agronomique de Toulouse, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Recherche Agronomique (INRA), Université de Pau et des Pays de l'Adour (UPPA), Veterinary Science Department, Faculty of Science and Technology, University of Trás-os-Montes and Alto Douro (Portugal), Department of Genetics and Biotechnology, University of Tras-os-Montes and Alto Douro, LAQV@REQUIMTE, DQ - Departamento de Química, PiLeJe Industrie, Sigma CLERMONT (Sigma CLERMONT), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Equipe MaQuaV, INATAA, Université Mentouri Constantine [Algérie] (UMC), Université Clermont Auvergne (UCA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Équipe Transformation et Elaboration des Produits Agro-Alimentaires (TEPA), Laboratoire de Nutrition et Technologies Alimentaires (LNTA)
Subjects: 0301 basic medicine, medicine.drug_class, Tetracycline, [SDV]Life Sciences [q-bio], 030106 microbiology, Antibiotics, Virulence, medicine.disease_cause, Bacterial resistance, Article, General Biochemistry, Genetics and Molecular Biology, antibiotics, Microbiology, 03 medical and health sciences, one health, Antibiotic resistance, SDG 3 - Good Health and Well-being, Immunology and Microbiology(all), Ampicillin, medicine, MALDI-TOF MS, lcsh:QH301-705.5, Gene, Escherichia coli, One health, Agricultural and Biological Sciences(all), General Immunology and Microbiology, biology, Biochemistry, Genetics and Molecular Biology(all), bacterial resistance, biomarkers, biology.organism_classification, 3. Good health, 030104 developmental biology, lcsh:Biology (General), General Agricultural and Biological Sciences, Biomarkers, Bacteria, medicine.drug
Abstract: Ação n.º: TC-14/2017 UIDB/50006/2020 The commensal bacteria Escherichia coli causes several intestinal and extra-intestinal diseases, since it has virulence factors that interfere in important cellular processes. These bacteria also have a great capacity to spread the resistance genes, sometimes to phylogenetically distant bacteria, which poses an additional threat to public health worldwide. Here, we aimed to use the analytical potential of MALDI-TOF mass spectrometry (MS) to characterize E. coli isolates and identify proteins associated closely with antibiotic resistance. Thirty strains of extended-spectrum beta-lactamase producing E. coli were sampled from various animals. The phenotypes of antibiotic resistance were determined according to Clinical and Laboratory Standards Institute (CLSI) methods, and they showed that all bacterial isolates were multi-resistant to trimethoprim-sulfamethoxazole, tetracycline, and ampicillin. To identify peptides characteristic of resistance to particular antibiotics, each strain was grown in the presence or absence of the different antibiotics, and then proteins were extracted from the cells. The protein fingerprints of the samples were determined by MALDI-TOF MS in linear mode over a mass range of 2 to 20 kDa. The spectra obtained were compared by using the ClinProTools bioinformatics software, using three machine learning classification algorithms. A putative species biomarker was also detected at a peak m/z of 4528.00. publishersversion published
Published: 2020

17. Benefits of the ipowder® extraction process applied to Melissa officinalis L.: improvement of antioxidant activity and in vitro gastro-intestinal release profile of rosmarinic acid

Author: Lucile Berthomier, Isabelle Ripoche, César Cotte, Sylvain Denis, Pierre Chalard, Monique Alric, Michel Dubourdeaux, Anaïs Escalon, Sandrine Chalancon, Valérie Bardot, Martin Leremboure, PiLeJe Industrie, Institut de Chimie de Clermont-Ferrand (ICCF), SIGMA Clermont (SIGMA Clermont)-Institut de Chimie du CNRS (INC)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Microbiologie Environnement Digestif Santé (MEDIS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Conception, Ingénierie et Développement de l'Aliment et du Médicament (CIDAM), Université d'Auvergne - Clermont-Ferrand I (UdA), Sigma CLERMONT (Sigma CLERMONT), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), and Université Clermont Auvergne (UCA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0301 basic medicine, Models, Anatomic, Antioxidant, DPPH, medicine.medical_treatment, [SDV]Life Sciences [q-bio], Drug Compounding, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, In Vitro Techniques, 01 natural sciences, Depsides, Melissa, Intestinal absorption, Antioxidants, 03 medical and health sciences, chemistry.chemical_compound, medicine, Humans, Food science, Active ingredient, 030109 nutrition & dietetics, Chemistry, Plant Extracts, Rosmarinic acid, 010401 analytical chemistry, Stomach, General Medicine, 0104 chemical sciences, Intestines, Plant Leaves, Phytochemical, Cinnamates, Officinalis, Melissa officinalis, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Food Science, Phytotherapy
Abstract: Export Date: 10 March 2020 Correspondence Address: Dubourdeaux, M.; PiLeJe Industrie, Naturopôle Nutrition Santé les TiolansFrance; email: m.dubourdeaux@pileje.com; International audience; The objective of this study was to evaluate the benefits of a new extraction process, the ipowder® technology, applied to Melissa officinalis L. Compared to M. officinalis ground dry leaves, the ipowder® had a similar phytochemical fingerprint but contained twice the concentration of rosmarinic acid (by HPTLC and HPLC) and had a two-fold greater antioxidant activity (DPPH* method). In vitro digestion experiments (TIM-1 model) showed better availability of rosmarinic acid for intestinal absorption with the ipowder® than with ground dry leaves, manifested by a three-fold reduction in the quantity of ingested product needed for delivery of the same amount of rosmarinic acid into the upper gastro-intestinal tract. This study shows that the ipowder® technology preserves all the original plant compounds intact while making some active ingredients more accessible and available to exert their effects. To obtain a given effect, the amount of ipowder® extract to ingest will therefore be lower; a reduction in the daily dosage will be more convenient for the patient and will improve patient compliance with supplementation.
Published: 2020

18. Streptococcus thermophilus: From yogurt starter to a new promising probiotic candidate?

Author: Sylvain Denis, Annie Dary-Mourot, Yvonne Roussel, Maira Junjua, Ophélie Uriot, Stéphanie Blanquet-Diot, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité de Recherches Animal et Fonctionnalités des Produits Animaux (URAFPA), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: 0301 basic medicine, Streptococcus thermophilus, Gram-positive bacteria, Microorganism, 030106 microbiology, Medicine (miscellaneous), Probiotic, Microbiology, law.invention, 03 medical and health sciences, chemistry.chemical_compound, Starter, law, medicine, TX341-641, Food science, Gastrointestinal survival, ComputingMilieux_MISCELLANEOUS, Nutrition and Dietetics, biology, Nutrition. Foods and food supply, Human gastrointestinal tract, food and beverages, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Lactic acid, health effect, 030104 developmental biology, medicine.anatomical_structure, chemistry, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Bacteria, S. thermophilus, Health effects, Food Science
Abstract: International audience; Probiotics are defined as live microorganisms that when administered in adequate amount confer a health benefit to the host. To be considered as a probiotic, a bacterial strain must not only be safe but should also survive in the human gastrointestinal tract and exert health benefits on its host. Streptococcus thermophilus is a Gram positive bacterium widely used in dairy fermentations for the production of yogurt and cheese. In contrast with other lactic acid bacteria, the probiotic status of S. thermophilus remains still questioned. This review gives an update of the human trials, in vivo assays in animal models and in vitro experiments, which have assessed the resistance of S. thermophilus to gastrointestinal stresses and have investigated its positive health effects. The underlying mechanisms of action are also described and the probiotic status of the bacterium is debated with respect to the available literature.
Published: 2017

19. Mycoplasma Chromosomal Transfer: A Distributive, Conjugative Process Creating an Infinite Variety of Mosaic Genomes

Author: Emilie Dordet-Frisoni, Marion Faucher, Eveline Sagné, Laurent-Xavier Nouvel, Florence Tardy, Christine Citti, Eric Baranowski, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Laboratoire de Physiopathologie Respiratoire, Université de la Méditerranée - Aix-Marseille 2, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Fonctionnement écologique et gestion durable des agrosystèmes bananiers et ananas (UR GECO), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Mycoplasmoses des Ruminants - UMR (MYCO), Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), and This work was supported by INRA and ENVT.
Subjects: Microbiology (medical), Mycoplasma agalactiae, [SDV]Life Sciences [q-bio], ved/biology.organism_classification_rank.species, lcsh:QR1-502, mycoplasmas, Chimeric gene, Biology, medicine.disease_cause, Genome, Microbiology, lcsh:Microbiology, 03 medical and health sciences, evolution, medicine, Model organism, Gene, 030304 developmental biology, Original Research, Genetics, 0303 health sciences, 030306 microbiology, ved/biology, Chromosome, Mycoplasma, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Horizontal gene transfer, horizontal gene transfer, chromosomal transfer, conjugation
Abstract: International audience; The capacity of Mycoplasmas to engage in horizontal gene transfers has recently been highlighted. Despite their small genome, some of these wall-less bacteria are able to exchange multiple, large portions of their chromosome via a conjugative mechanism that does not conform to canonical Hfr/oriT models. To understand the exact features underlying mycoplasma chromosomal transfer (MCT), extensive genomic analyses were performed at the nucleotide level, using individual mating progenies derived from our model organism, Mycoplasma agalactiae. Genome reconstruction showed that MCT resulted in the distributive transfer of multiple chromosomal DNA fragments and generated progenies composed of a variety of mosaic genomes, each being unique. Analyses of macro-and micro-events resulting from MCT revealed that the vast majority of the acquired fragments were unrelated and co-transferred independently from the selection marker, these resulted in up to 17% of the genome being exchanged. Housekeeping and accessory genes were equally affected by MCT, with up to 35 CDSs being gained or lost. This efficient HGT process also created a number of chimeric genes and genetic micro-variations that may impact gene regulation and/or expression. Our study unraveled the tremendous plasticity of M. agalactiae genome and point toward MCT as a major player in diversification and adaptation to changing environments, offering a significant advantage to this minimal pathogen.
Published: 2019

20. Nitrogen metabolism in rumen bacteria can be characterised by their N isotopic signature

Author: Gonzalo Cantalapiedra-Hijar, G. Martinez-Fernandez, Diego P. Morgavi, Christopher S. McSweeney, C. Chantelauze, E. Forano, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Commonwealth Scientific and Industrial Research Organisation (CSIRO), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, INRA-CSIRO linkage programme, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, ProdInra, Archive Ouverte, Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: animal structures, 040301 veterinary sciences, Proteolysis, [SDV]Life Sciences [q-bio], ruminant, ammonia, fractionnement isotopique, 0403 veterinary science, Isotopic signature, Rumen, medicine, Food science, Nitrogen cycle, Organism, biology, medicine.diagnostic_test, Chemistry, 15N, 0402 animal and dairy science, 04 agricultural and veterinary sciences, Metabolism, biology.organism_classification, 040201 dairy & animal science, ammoniac, [SDV] Life Sciences [q-bio], isotopic fractionation, Pure culture, Bacteria
Abstract: The N use efficiency (NUE) of ruminants is negatively correlated to the natural 15N enrichment of ruminants’ tissues over their diets (Δ15Nanimal-diet). The metabolism of rumen bacteria, which strongly discriminates against 15N utilisation, may contribute to this link but little is known about the role of individual bacteria. In this study, we characterised the Δ15N of three metabolically different rumen bacteria, a cellulolytic ammonia-consuming, a hyperammonia producing and a proteolytic organism, grown in pure culture with different N sources and levels. The N isotopic signatures significantly changed across the 3 rumen bacteria. Although we failed to observe a higher Δ15Nbacteria-substrate when proteolysis and ammonia production was favoured, our results confirm a strong 15N depletion with the ammonia-consuming bacterium. This may suggest that 15N depleted ammonia-consuming bacteria improves the NUE in the rumen.
Published: 2019

21. Experimental models to study intestinal microbes–mucus interactions in health and disease

Author: Raphaële Gresse, Benoit Chassaing, Lucie Etienne-Mesmin, Nathalie Juge, Kim De Paepe, Mickaël Desvaux, Stéphanie Blanquet-Diot, Thomas Sauvaitre, Tom Van de Wiele, Evelyne Forano, Stephanie Schüller, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Infection, Immunity and Inflammation, Georgia State University, University System of Georgia (USG)-University System of Georgia (USG), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Quadram Institute, Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), North Georgia College & State University, Universiteit Gent = Ghent University (UGENT), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), University of East Anglia [Norwich] (UEA), Biotechnology and Biological Sciences Research Council (BBSRC), Biotechnology and Biological Sciences Research Council (BBSRC) BBS/E/F/00044452, INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Universiteit Gent = Ghent University [Belgium] (UGENT), and Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV]Life Sciences [q-bio], experimental models, Context (language use), Disease, In Vitro Techniques, Gut flora, Microbiology, Mice, 03 medical and health sciences, fluids and secretions, intestinal mucus, Animals, Homeostasis, Humans, Microbiome, Intestinal Mucosa, 030304 developmental biology, mucin O-glycosylation, 0303 health sciences, Gastrointestinal tract, Host Microbial Interactions, biology, gut microbiota, 030306 microbiology, Mucin, Mucins, biology.organism_classification, Intestinal epithelium, Mucus, Gastrointestinal Microbiome, Rats, Gastrointestinal Tract, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Models, Animal, Microbial Interactions
Abstract: International audience; One sentence summary: The review summarises the state of the art for studying gut microbes-mucus interactions using in vitro, ex vivo and in vivo experimental models. Editor: Ehud Banin † These authors contributed equally to this work ABSTRACT A close symbiotic relationship exists between the intestinal microbiota and its host. A critical component of gut homeostasis is the presence of a mucus layer covering the gastrointestinal tract. Mucus is a viscoelastic gel at the interface between the luminal content and the host tissue that provides a habitat to the gut microbiota and protects the intestinal epithelium. The review starts by setting up the biological context underpinning the need for experimental models to study gut bacteria-mucus interactions in the digestive environment. We provide an overview of the structure and function of intestinal mucus and mucins, their interactions with intestinal bacteria (including commensal, probiotics and pathogenic microorganisms) and their role in modulating health and disease states. We then describe the characteristics and potentials of experimental models currently available to study the mechanisms underpinning the interaction of mucus with gut microbes, including in vitro, ex vivo and in vivo models. We then discuss the limitations and challenges facing this field of research.
Published: 2019

22. Can dynamic in vitro digestion systems mimic the physiological reality?

Author: Didier Dupont, Alan R. Mackie, Maria J. Ferrua, Stéphanie Blanquet-Diot, R Havenaar, Beatriz Miralles, Monique Alric, Amélie Deglaire, Isidra Recio, P Van den Abbeele, Sylvain Denis, J Lelieveld, C Cueva, Olivia Ménard, Mans Minekus, Massimo Marzorati, Gail M. Bornhorst, Science et Technologie du Lait et de l'Oeuf (STLO), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Université Clermont Auvergne (UCA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, University of California [Davis] (UC Davis), University of California, Universidad Autonoma de Madrid (UAM), Fonterra Research Centre, New Zealand Dairy Research Institute, Triskelion, University of Leeds, Universiteit Gent [Ghent], Cargill R&D Centre Europe BVBA, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Universiteit Gent = Ghent University [Belgium] (UGENT), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), University of California (UC), Universidad Autónoma de Madrid (UAM), and Universiteit Gent = Ghent University (UGENT)
Subjects: 0301 basic medicine, Dynamic in vitro digestion, Colon, Computer science, HUMULUS-LUPULUS L, education, 01 natural sciences, Industrial and Manufacturing Engineering, 03 medical and health sciences, Human health, In vivo, PROBIOTIC YEAST, GUT MODEL, COMPUTER-CONTROLLED MODEL, HUMAN-MILK, Gastrointestinal tract, MICROBIAL COMMUNITY, food, Stomach, 010401 analytical chemistry, Small intestine, General Medicine, In vitro digestion, 0104 chemical sciences, GASTRIC DIGESTION, 030104 developmental biology, Dynamic models, Food, Ph regulation, HUMAN LARGE-INTESTINE, GASTROINTESTINAL MODEL, METABOLITE PRODUCTION, Digestive tract, Biochemical engineering, Digestion, small intestine, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, stomach, Food Science
Abstract: During the last decade, there has been a growing interest in understanding the fate of food during digestion in the gastrointestinal tract in order to strengthen the possible effects of food on human health. Ideally, food digestion should be studied in vivo on humans but this is not always ethically and financially possible. Therefore simple static in vitro digestion models mimicking the gastrointestinal tract have been proposed as alternatives to in vivo experiments but these models are quite basic and hardly recreate the complexity of the digestive tract. In contrast, dynamic models that allow pH regulation, flow of the food and injection in real time of digestive enzymes in the different compartments of the gastrointestinal tract are more promising to accurately mimic the digestive process. Most of the systems developed so far have been compared for their performances to in vivo data obtained on animals and/or humans. The objective of this article is to review the validation towards in vivo data of some of the dynamic digestion systems currently available in order to determine what aspects of food digestion they are able to mimic. Eight dynamic digestion systems are presented as well as their validation towards in vivo data. Advantages and limits of each simulator is discussed. This is the result of a cooperative international effort made by some of the scientists involved in Infogest, an international network on food digestion.
Published: 2019

23. Procyanidin—Cell Wall Interactions within Apple Matrices Decrease the Metabolization of Procyanidins by the Human Gut Microbiota and the Anti-Inflammatory Effect of the Resulting Microbial Metabolome In Vitro

Author: Claire Dufour, Pascale Lepercq, Pauline Auffret, Pascale Mosoni, Catherine M.G.C. Renard, Philippe Ruiz, Sophie Comtet-Marre, Priscilla Bagano Vilas Boas, Jean-Marc Chatel, Carine Le Bourvellec, Romain Bott, Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Avignon Université (AU)-Institut National de la Recherche Agronomique (INRA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), UMR 241 EIO, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Département Caractérisation et Elaboration des Produits Issus de l'Agriculture (CEPIA), Institut National de la Recherche Agronomique (INRA), Avignon Université (AU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Ecosystèmes Insulaires Océaniens (UMR 241) (EIO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD), Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université de la Polynésie Française (UPF)-Institut Louis Malardé [Papeete] (ILM), and Institut de Recherche pour le Développement (IRD)-Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: 0301 basic medicine, procédé agroalimentaire, [SDV]Life Sciences [q-bio], Anti-Inflammatory Agents, in vitro batch fermentation, polyphenols, dietary fiber, 16S metabarcoding, metabotype, Gut flora, Cell Wall, fermentation in vitro, chemistry.chemical_classification, Nutrition and Dietetics, biology, Chemistry, solvent free microwave extraction (sfem), 04 agricultural and veterinary sciences, 040401 food science, Proanthocyanidin, Biochemistry, extraction d'adn, Malus, lcsh:Nutrition. Foods and food supply, paroi cellulaire végétale, composition phénolique, pcr quantitative, lcsh:TX341-641, Polysaccharide, Article, Cell wall, 03 medical and health sciences, polyphénol, 0404 agricultural biotechnology, Metabolome, Carbohydrate fermentation, Humans, procyanidine, Proanthocyanidins, 030109 nutrition & dietetics, Bacteria, purée de fruit, biology.organism_classification, Gastrointestinal Microbiome, Polyphenol, Fruit, Fermentation, extraction, métabolite microbien, malus domestica borkh, Food Science
Abstract: B-type oligomeric procyanidins in apples constitute an important source of polyphenols in the human diet. Their role in health is not known, although it is suggested that they generate beneficial bioactive compounds upon metabolization by the gut microbiota. During apple processing, procyanidins interact with cell-wall polysaccharides and form stable complexes. These interactions need to be taken into consideration in order to better assess the biological effects of fruit constituents. Our objectives were to evaluate the impact of these interactions on the microbial metabolization of cell walls and procyanidins, and to investigate the potential anti-inflammatory activity of the resulting metabolome, in addition to analyzing the taxonomical changes which the microbiota undergo. In vitro fermentation of three model apple matrices with microbiota from 4 healthy donors showed that the binding of procyanidins to cell-wall polysaccharides, whether covalently or non-covalently, substantially reduced procyanidin degradation. Although cell wall-unbound procyanidins negatively affected carbohydrate fermentation, they generated more hydroxyphenylvaleric acid than bound procyanidins, and increased the abundance of Adlercreutzia and Gordonibacter genera. The best results in terms of production of anti-inflammatory bioactive metabolites were observed from the apple matrix with no bonds between procyanidins and cell wall polysaccharides, although the matrix with non-covalent bonds was not far behind.
Published: 2019

24. Identification and prevalence of in vivo -induced genes in enterohaemorrhagic Escherichia coli

Author: Annie Garrivier, Estelle Loukiadis, Simon Le Hello, Grégory Jubelin, Patricia Mariani-Kurkdjian, Laetitia Fabre, François Gravey, Marion Gardette, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre National de Référence - National Reference Center Escherichia coli, Shigella et Salmonella (CNR-ESS), Institut Pasteur [Paris], Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU), AP-HP Hôpital universitaire Robert-Debré [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), This work was supported by the Institut Pasteur, Ministère de l’Agriculture et de l'Alimentation, Santé Publique France, INRA., Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut Pasteur [Paris] (IP), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Centre National de Référence des Escherichia coli, Shigella et Salmonella - Bactéries pathogènes entériques (CNR-ESS), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: Microbiology (medical), Serotype, gene prevalence, rivet, Virulence Factors, Immunology, Virulence, Gene Expression, ehec, Serogroup, Microbiology, Polymerase Chain Reaction, Virulence factor, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Mice, STX2, Stress, Physiological, Prevalence, Animals, lcsh:RC109-216, intestinal pathogen, Gene, Escherichia coli Infections, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Intimin, 0303 health sciences, biology, 030306 microbiology, Escherichia coli Proteins, Shiga toxin, stress response, biochemical phenomena, metabolism, and nutrition, bacterial infections and mycoses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Bacterial adhesin, virulence, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Enterohemorrhagic Escherichia coli, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, biology.protein, Parasitology, metabolism, Research Paper
Abstract: Epub 2019 Feb 26; International audience; Enterohaemorrhagic Escherichia coli (EHEC) are foodborne pathogens responsible for bloody diarrhoea and renal failure in humans. While Shiga toxin (Stx) is the cardinal virulence factor of EHEC, its production by E. coli is not sufficient to cause disease and many Shiga-toxin producing E. coli (STEC) strains have never been implicated in human infection. So far, the pathophysiology of EHEC infection is not fully understood and more knowledge is needed to characterize the "auxiliary" factors that enable a STEC strain to cause disease in humans. In this study, we applied a recombinase-based in vivo expression technology (RIVET) to the EHEC reference strain EDL933 in order to identify genes specifically induced during the infectious process, using mouse as an infection model. We identified 31 in vivo-induced (ivi) genes having functions related to metabolism, stress adaptive response and bacterial virulence or fitness. Eight of the 31 ivi genes were found to be heterogeneously distributed in EHEC strains circulating in France these last years. In addition, they are more prevalent in strains from the TOP 7 priority serotypes and particularly strains carrying significant virulence determinants such as Stx2 and intimin adhesin. This work sheds further light on bacterial determinants over-expressed in vivo during infection that may contribute to the potential of STEC strains to cause disease in humans.
Published: 2019

25. Mycoplasmas under experimental antimicrobial selection: The unpredicted contribution of horizontal chromosomal transfer

Author: Eric Baranowski, Marc-Serge Marenda, Marion Faucher, Emilie Dordet-Frisoni, Marie-Claude Hygonenq, Eveline Sagné, Laurent-Xavier Nouvel, Florence Tardy, Christine Citti, Interactions hôtes-agents pathogènes [Toulouse] (IHAP), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Mycoplasmoses des Ruminants - UMR (MYCO), Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), University of Melbourne, Asia-Pacific Centre for Animal Health, Faculty of Veterinary Science, This work was supported by National Institute for Agricultural Research (INRA, institut.inra.fr), National Veterinary School of Toulouse (ENVT, Laboratoire de Physiopathologie Respiratoire, Université de la Méditerranée - Aix-Marseille 2, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Ecole Nationale Vétérinaire de Toulouse (ENVT), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Cancer Research, Mycoplasma agalactiae, ved/biology.organism_classification_rank.species, Gene Transfer, QH426-470, medicine.disease_cause, Genome, 0302 clinical medicine, Mycoplasma, Genetics (clinical), Genetics, 0303 health sciences, Enrofloxacin, Genomics, Horizontal gene transfer, Anti-Bacterial Agents, Research Article, Fluoroquinolones, Evolutionary Processes, Gene Transfer, Horizontal, Genetic loci, Mollicutes, Mycology, Biology, Research and Analysis Methods, Genome Complexity, Evolution, Molecular, 03 medical and health sciences, Bacterial Proteins, medicine, Selection, Genetic, Molecular Biology Techniques, Gene, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Comparative genomics, Evolutionary Biology, Bacteria, ved/biology, Organisms, Biology and Life Sciences, Computational Biology, Single nucleotide polymorphisms, Genome analysis, Comparative Genomics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Fungal evolution, Mobile genetic elements, 030217 neurology & neurosurgery, Cloning
Abstract: Horizontal Gene Transfer was long thought to be marginal in Mycoplasma a large group of wall-less bacteria often portrayed as minimal cells because of their reduced genomes (ca. 0.5 to 2.0 Mb) and their limited metabolic pathways. This view was recently challenged by the discovery of conjugative exchanges of large chromosomal fragments that equally affected all parts of the chromosome via an unconventional mechanism, so that the whole mycoplasma genome is potentially mobile. By combining next generation sequencing to classical mating and evolutionary experiments, the current study further explored the contribution and impact of this phenomenon on mycoplasma evolution and adaptation using the fluoroquinolone enrofloxacin (Enro), for selective pressure and the ruminant pathogen Mycoplasma agalactiae, as a model organism. For this purpose, we generated isogenic lineages that displayed different combination of spontaneous mutations in Enro target genes (gyrA, gyrB, parC and parE) in association to gradual level of resistance to Enro. We then tested whether these mutations can be acquired by a susceptible population via conjugative chromosomal transfer knowing that, in our model organism, the 4 target genes are scattered in three distinct and distant loci. Our data show that under antibiotic selective pressure, the time scale of the mutational pathway leading to high-level of Enro resistance can be readily compressed into a single conjugative step, in which several EnroR alleles were transferred from resistant to susceptible mycoplasma cells. In addition to acting as an accelerator for antimicrobial dissemination, mycoplasma chromosomal transfer reshuffled genomes beyond expectations and created a mosaic of resistant sub-populations with unpredicted and unrelated features. Our findings provide insights into the process that may drive evolution and adaptability of several pathogenic Mycoplasma spp. via an unconventional conjugative mechanism., Author summary Genome downsizing is often viewed as a degenerative process of evolution. Such erosion has left current mycoplasmas with a minimal genome: for some species its size barely exceeds the amount of information needed for sustaining autonomous life. Despite such limitations, these simple bacteria showcase a baffling capacity for adaptation to complex environments such as that provided by the animal host. By using the enrofloxacin antibiotic as selective pressure, we performed a genome scale analysis of macro- and micro-events leading to antimicrobial resistance in mycoplasmas. Sexually competent cells were found to shortcut this process by using an unconventional mechanism of chromosomal transfer driving massive exchanges of DNA materials. Remarkably, this powerful mechanism was associated with a profound genomic reorganization that reshuffled parental features and created mosaicism. This finding emphasizes the extraordinary adaptability of some pathogenic Mycoplasma spp. and provides major insights into the processes that contribute to shaping the evolution of their minimal genome. While unconventional conjugative mechanisms are being documented in more complex bacteria, the reduced mycoplasma genome may provide a simplified model to study mosaicism and its role in bacterial evolution.
Published: 2019

26. Does the goat phenotype in terms of feeding behavior, rumen dynamics and production traits, shape the rumen microbiota composition? First case study

Author: Gomes, Pierre, Mosoni, Pascale, Taghipoor, Masoomeh, Bouchez, Olivier, Berthelot, Valérie, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Modélisation Systémique Appliquée aux Ruminants (MoSAR), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Génome et Transcriptome - Plateforme Génomique, and Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs]
Published: 2019

27. A mix of dietary fermentable fibers improves lipids handling by the liver of overfed minipigs

Author: Daniel Béchet, Didier Rémond, Jérémie David, Michel Hébraud, Isabelle Savary-Auzeloux, Noureddine Hafnaoui, Benoit Cohade, Ahmed Ben Mohamed, Sergio Polakof, Christophe Chambon, Frédéric Capel, Dominique Dardevet, Joël Doré, Carole Migné, Thierry Sayd, Cécile Coudy-Gandilhon, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), INRA, France (AlimH research department), INRA, France (CEPIA research department), and INRA, France (MICA research department)
Subjects: 0301 basic medicine, Sucrose, Endocrinology, Diabetes and Metabolism, Clinical Biochemistry, fibre alimentaire, Biochemistry, chemistry.chemical_compound, Overnutrition, 0302 clinical medicine, Nonalcoholic fatty liver disease, mini-pig proteomic, Resistant starch, protéomique, 2. Zero hunger, Nutrition and Dietetics, Short-chain fatty acid, dietary fibre, Inulin, dietary fiber, foie, Lipogenesis, Pectins, Swine, Miniature, Female, medicine.medical_specialty, food.ingredient, short chain fatty acid, 030209 endocrinology & metabolism, Carbohydrate metabolism, Diet, High-Fat, liver, acide gras à chaîne courte, 03 medical and health sciences, food, proteomics, lipid, Internal medicine, medicine, Animals, Molecular Biology, lipide, Cholesterol, Proteins, swine, Metabolism, Fatty Acids, Volatile, Lipid Metabolism, medicine.disease, fibre fermentescible, 030104 developmental biology, Endocrinology, Gene Expression Regulation, chemistry, Fermentation, liver function tests, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, porc
Abstract: Obesity induced by overfeeding ultimately can lead to nonalcoholic fatty liver disease, whereas dietary fiber consumption is known to have a beneficial effect. We aimed to determine if a supplementation of a mix of fibers (inulin, resistant starch and pectin) could limit or alleviate overfeeding-induced metabolic perturbations. Twenty female minipigs were fed with a control diet (C) or an enriched fat/sucrose diet supplemented (O + F) or not (O) with fibers. Between 0 and 56 days of overfeeding, insulin (+88%), HOMA (+102%), cholesterol (+45%) and lactate (+63%) were increased, without any beneficial effect of fibers supplementation. However, fibers supplementation limited body weight gain (vs. O, −15% at D56) and the accumulation of hepatic lipids droplets induced by overfeeding. This could be explained by a decreased lipids transport potential (−50% FABP1 mRNA, O + F vs. O) inducing a down-regulation of regulatory elements of lipids metabolism / lipogenesis (−36% SREBP1c mRNA, O + F vs. O) but not to an increased oxidation (O + F not different from O and C for proteins and mRNA measured). Glucose metabolism was also differentially regulated by fibers supplementation, with an increased net hepatic release of glucose in the fasted state (diet × time effect, P
Published: 2019

28. Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Author: Brown, Peter, Tan, Aik-Choon, El-Esawi, Mohamed A., Liehr, Thomas, Blanck, Oliver, Gladue, Douglas, Almeida, Gabriel M. F., Cernava, Tomislav, Sorzano, Carlos, Yeung, Andy W. K., Engel, Michael S., Chandrasekaran, -., Muth, Thilo, Staege, Martin S., Daulatabad, Swapna V., Widera, Darius, Zhang, Junpeng, Meule, Adrian, Honjo, Ken, Pourret, Olivier, Yin, Cong-Cong, Zhang, Zhongheng, Cascella, Marco, Flegel, Willy A., Goodyear, Carl S., Raaj, Mark J., Bukowy-Bieryllo, Zuzanna, Campana, Luca G., Kurniawan, Nicholas A., Lalaouna, David, Huttner, Felix J., Ammerman, Brooke A., Ehret, Felix, Cobine, Paul A., Tan, Ene-Choo, Han, Hyemin M., Xia, Wenfeng F., Mc Crum, Christopher, Dings, Ruud P. M., Marinello, Francesco, Nilsson, Henrik, Nixon, Brett, Voskarides, Konstantinos, Yang, Long, Costa, Vincent D., Bengtsson-Palme, Johan, Bradshaw, William, Grimm, Dominik G., Kumar, Nitin, Martis, Elvis, Prieto, Daniel, Sabnis, Sandeep C., Amer, Said E. D. R., Liew, Alan W. C., Perco, Paul, Rahimi, Farid, Riva, Guiseppe, Zhang, Chongxing, Devkota, Hari P., Ogami, Koichi, Basharat, Zarrin, Fierz, Walter, Siebers, Robert, Tan, Kok-Hian, Boehme, Karen A., Brenneisen, Peter, Brown, James A. L., Dalrymple, Brian P., Harvey, David J., Ng, Grace, Werten, Sebastiaan, Bleackley, Mark R., Dai, Zhanwu, Dhariwal, Raman, Gelfer, Yael, Hartmann, Marcus D., Miotla, Pawel, Tamalan, Radu, Pragashnie Govender (nee' Naidoo), Gurney-Champion, Oliver J., Kauppila, Joonas H., Zhang, Xiaolei L., Echeverria, Natalia, Subhash, Santhilal, Salimon, Hannes, Tofani, Marco, Bae, Taeok, Bosch, Oliver, Cuiv, Paraic O., Danchin, Antoine, Diouf, Barthélémy, Eerola, Tuomas, Evangelou, Evangelos, Filipp, Fabian V., Klump, Hannes, Kurgan, Lukasz, Smith, Simon S., Terrier, Olivier, Tuttle, Neil, Ascher, David B., Janga, Sarath C., Alaux, Cédric, Zhou, Yaoq, Forano, Evelyne, Grifﬁth University, University of Colorado, University of Colorado [Boulder], Tanta University, Friedrich Schiller University Jena [Jena, Germany], University Medical Center Schleswig-Holstein, European Biological Control Laboratory, USDA-ARS (EBCL - USDA ARS), Department of Biological and Environmental Science [Jyväskylä], University of Jyväskylä (JYU), Graz University of Technology, Partenaires INRAE, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of Hong Kong, University of Kansas, State University of New York (SUNY), Robert Koch Institute [Berlin] (RKI), Martin-Luther-University Halle-Wittenberg, Indiana University, Indiana University System, University of Reading (UOR), Dali University, Ludwig Maximilians University of Munich, Schoen Clin Roseneck, University of Tsukuba, Institut Polytechnique LaSalle Beauvais, Henry Ford Hlth System, Zhejiang University, Fondazione IRCCS Istituto Nazionale dei Tumori, National Institutes of Health, University of Glasgow, Polish Academy of Sciences (PAN), Universitad de Padua, Eindhoven University of Technology, IBMC, Heidelberg University, University of Notre Dame, Massachusetts General Hospital, Massachusetts General Hospital [Boston], Auburn University (AU), KK Women’s and Children’s Hospital (KKH), University of Alabama, Department of Finance, University College of London [London] (UCL), Maastricht University [Maastricht], University of Arkansas, Dept Biol & Environm Sci, University of Gothenburg (GU), University of Newcastle (UoN), University of Cyprus, Shandong Agricultural University (SDAU), National Institute of Mental Health, University of Wisconsin-Madison, University of Oxford [Oxford], University of Applied Sciences of Weihenstephan, University of Michigan [Ann Arbor], University of Michigan System, Bombay Coll. Pharm., Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Gem Hosp & Res. Ctr, Fac. Sci., Dept. Zool., Charles University, Innsbruck Medical University, Australian National University (ANU), Università Cattolica del Sacro Cuore, Shandong University, Kumamoto University, Nagoya University, University of Karachi, Labomed Zentrum Dr Risch, MED, Université ouverte de Grèce, University of Freiburg [Freiburg], Heinrich-Heine-Universität Düsseldorf [Düsseldorf], National University of Ireland [Galway] (NUI Galway), University of Western Australia, La Trobe University, Université de Bordeaux (UB), Agr & Agri Food Canada, Agr & Agri Food Canada, Agr & Agroalimentaire Canada, St. George’s Hospital University, Max-Planck-Institut, Medical University in Lublin, National Institute of Research and Development for Cryogenic and Isotopic Technologies ICSI Rm. Valcea, University of KwaZulu-Natal (UKZN), Institute of cancer research, Karolinska Institutet [Stockholm], Wenzhou Medical University, Universidad de la República, Charité - Universitätsmedizin Berlin / Charite - University Medicine Berlin, Hospital Bambino Gesù, University of Regensburg, Central Queensland University (CQU), Translat. Res. Inst., Institut Cochin (IC UM3 (UMR 8104 / U1016)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), St Jude Children's Research Hospital, Durham University, University of Ioannina, Sch Life Sci Weihenstephan, Technical University of Munich (TUM), German Research Center for Environmental Health - Helmholtz Center München (GmbH), Essen University Hospital, Virginia Commonwealth University (VCU), UR 406 Abeilles & Environnement, Institut National de la Recherche Agronomique (INRA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), and Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix
Subjects: [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences
Abstract: Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.
Published: 2019

29. Biofilm formation of listeria monocytogenes strains under food processing environments and pan-genome-wide association study

Author: Bo-Hyung Lee, Sophie Cole, Stéphanie Badel-Berchoux, Laurent Guillier, Benjamin Felix, Nicolas Krezdorn, Michel Hébraud, Thierry Bernardi, Ibrahim Sultan, Pascal Piveteau, Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), BioFilm Control SAS, Biopôle Clermont - Limagne, GenXpro GmBH, FIZ, French Agency Food Environment and Occupation Health and Safety, Université Paris Est, GenXpro GmBH, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de la Recherche Agronomique (INRA), UR 1466 Optimisation des procédés en agriculture, agroalimentaire et environnement, European Union (EU) 641984, Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Optimisation des procédés en Agriculture, Agroalimentaire et Environnement (UR OPAALE), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Ecole Doctorale Science Vie Sante Agronomie Environnement, Université Clermont Auvergne (UCA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), and Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix
Subjects: Microbiology (medical), intraspecies diversity, [SDV]Life Sciences [q-bio], biofilm, Listeria monocytogenes, pan-genome-wide association study, adhesion, NaCl, nutrient deficiency, clonal complex, lcsh:QR1-502, Biology, medicine.disease_cause, 7. Clean energy, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Food chain, adhésion, Nutrient, Genotype, medicine, Food science, Original Research, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, 030306 microbiology, Biofilm, Pan-genome, biochemical phenomena, metabolism, and nutrition, Transformation (genetics), listeria monocytogènes, Food contaminant
Abstract: International audience; Concerns about food contamination by Listeria monocytogenes are on the rise with increasing consumption of ready-to-eat foods. Biofilm production of L. monocytogenes is presumed to be one of the ways that confer its increased resistance and persistence in the food chain. In this study, a collection of isolates from foods and food processing environments (FPEs) representing persistent, prevalent, and rarely detected genotypes was evaluated for biofilm forming capacities including adhesion and sessile biomass production under diverse environmental conditions. The quantity of sessile biomass varied according to growth conditions, lineage, serotype as well as genotype but association of clonal complex (CC) 26 genotype with biofilm production was evidenced under cold temperature. In general, relative biofilm productivity of each strain varied inconsistently across growth conditions. Under our experimental conditions, there were no clear associations between biofilm formation efficiency and persistent or prevalent genotypes. Distinct extrinsic factors affected specific steps of biofilm formation. Sudden nutrient deprivation enhanced cellular adhesion while a prolonged nutrient deficiency impeded biofilm maturation. Salt addition increased biofilm production, moreover, nutrient limitation supplemented by salt significantly stimulated biofilm formation. Pan-genome-wide association study (Pan-GWAS) assessed genetic composition with regard to biofilm phenotypes for the first time. The number of reported genes differed depending on the growth conditions and the number of common genes was low. However, a broad overview of the ontology contents revealed similar patterns regardless of the conditions. Functional analysis showed that functions related to transformation/competence and surface proteins including Internalins were highly enriched.
Published: 2019

30. Listeria monocytogenes Biofilm Adaptation to Different Temperatures Seen Through Shotgun Proteomics

Author: Santos, Tiago, Viala, Didier, Chambon, Christophe, Esbelin, Julia, Hébraud, Michel, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Plateforme d'Exploration du Métabolisme, European Union's Horizon 2020 research and Innovation programme under the Marie-Slodowska Curie grant 641984, Agence Nationale de la Recherche (ANR) (France) as part of an EcoSec contract, Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Plateforme Exploration du Métabolisme (PFEM), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-MetaboHUB-Clermont, MetaboHUB-MetaboHUB, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), and Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix
Subjects: subproteomes, shotgun proteomics, temperature adaptation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.IDA]Life Sciences [q-bio]/Food engineering, listeria monocytogenes, biofilm, listeria monocytogènes, protéome, Listeria monocytogenes, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Nutrition, Original Research
Abstract: International audience; Listeria monocytogenes is a foodborne pathogen that can cause invasive severe human illness (listeriosis) in susceptible patients. Most human listeriosis cases appear to be caused by consumption of refrigerated ready-to-eat foods. Although initial contamination levels in foods are usually low, the ability of these bacteria to survive and multiply at low temperatures allows it to reach levels high enough to cause disease. This study explores the set of proteins that might have an association with L. monocytogenes adaptation to different temperatures. Cultures were grown in biofilm, the most widespread mode of growth in natural and industrial realms. Protein extractions were performed from three different growth temperatures (10, 25, and 37°C) and two growth phases (early stage and mature biofilm). L. monocytogenes subproteomes were targeted using three extraction methods: trypsin-enzymatic shaving, biotin-labeling and cell fractionation. The different subproteomes obtained were separated and analyzed by shotgun proteomics using high-performance liquid chromatography combined with tandem mass spectrometry (LC-OrbiTrap LTQVelos, ThermoFisher Scientific). A total of 141 (biotinylation), 98 (shaving) and 910 (fractionation) proteins were identified. Throughout the 920 unique proteins identified, many are connected to basic cell functions, but some are linked with thermoregulation. We observed some noteworthy protein abundance shifts associated with the major adaptation to cold mechanisms present in L. monocytogenes, namely: the role of ribosomes and the stressosome with a higher abundance of the general stress protein Ctc (Rl25) and the general stress transcription factor sigma B (σB), changes in cell fluidity and motility seen by higher levels of foldase protein PrsA2 and flagellin (FlaA), the uptake of osmolytes with a higher abundance of glycine betaine (GbuB) and carnitine transporters (OpucA), and the relevance of the overexpression of chaperone proteins such as cold shock proteins (CspLA and Dps). As for 37°C, we observed a significantly higher percentage of proteins associated with transcriptional or translational activity present in higher abundance upon comparison with the colder settings. These contrasts of protein expression throughout several conditions will enrich databases and help to model the regulatory circuitry that drives adaptation of L. monocytogenes to environments.
Published: 2019

31. Comparison of conventional plating, PMA-qPCR, and flow cytometry for the determination of viable enterotoxigenic Escherichia coli along a gastrointestinal in vitro model

Author: T. Van de Wiele, Françoise Leriche, S. Denis, Stéphanie Blanquet-Diot, Charlène Roussel, S. Chalancon, Wessam Galia, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Center for Microbial Ecology and Technology (CMET), Universiteit Gent = Ghent University [Belgium] (UGENT), Laboratoire d'Ecologie Microbienne - UMR 5557 (LEM), Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Ecole Nationale Vétérinaire de Lyon (ENVL), Unité Mixte de Recherche sur le Fromage (UMRF), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Ministere de la Recherche (France), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Vétérinaire de Lyon (ENVL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Unité Mixte de Recherche Fromagère (UMRF), Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche sur le Fromage - UMR 545 (UMRF), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Université Clermont Auvergne (UCA), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Universiteit Gent = Ghent University (UGENT), Université de Lyon-Université de Lyon-Ecole Nationale Vétérinaire de Lyon (ENVL)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), and Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: 0301 basic medicine, enterotoxigenic Escherichia coli, [SDV]Life Sciences [q-bio], 030106 microbiology, Population, Colony Count, Microbial, Virulence, Biology, Real-Time Polymerase Chain Reaction, medicine.disease_cause, Models, Biological, Applied Microbiology and Biotechnology, plating, Microbiology, Flow cytometry, 03 medical and health sciences, Propidium monoazide, digestive environment, Enterotoxigenic Escherichia coli, medicine, Humans, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, education, ComputingMilieux_MISCELLANEOUS, education.field_of_study, Microbial Viability, medicine.diagnostic_test, viability, flow cytometry, PMA-qPCR, General Medicine, biology.organism_classification, In vitro, Gastrointestinal Tract, Real-time polymerase chain reaction, Bacteria, Biotechnology
Abstract: International audience; Recent technological advances for bacterial viability assessment using molecular methods or flow cytometry can provide meaningful interest for the demarcation between live and dead microorganisms. Nonetheless, these methods have been scarcely applied to foodborne pathogens and never for directly assessing their viability within the human digestive environment. The purpose of this study was to compare two methods based on membrane integrity (propidium monoazide (PMA)q-PCR and Live/Dead flow cytometry) and the classical plate-count method to determine the viability of a common foodborne pathogen, enterotoxigenic Escherichia coli (ETEC), during its transit trough simulated human gastrointestinal environment. Viable ETEC counts in the gastric and small intestinal compartments of the gastrointestinal TIM model indicated a consensus between the three tested methods (PMA-qPCR, flow cytometry, and plate counts). In a further step, flow cytometry analysis appeared as the preferred method to elucidate ETEC physiological states in the in vitro digestive environment by discriminating four subpopulations, while PMA-qPCR can only distinguish two. The defined viable/altered ETEC population was found during all in vitro digestions, but mainly in the gastric compartment. Being able to discriminate the particular physiological states of pathogenic microorganisms in the digestive environment is of high interest, because if some cells are not observable on culture media, they might keep their ability to express virulence functions.
Published: 2018

32. Addressing global ruminant agricultural challenges through understanding the rumen microbiome: Past, present and future

Author: Huws, Sharon A., Creevey, Christopher J., Oyama, Linda B., Mizrahi, Itzhak, Denman, Stuart E., Popova, Milka, Muñoz-Tamayo, Rafael, Forano, Evelyne, Waters, Sinead M., Hess, Matthias, Tapio, Ilma, Smidt, Hauke, Krizsan, Sophie J., Yáñez-Ruiz, David R., Belanche, Alejandro, Guan, Leluo, Gruninger, Robert J., McAllister, Tim A., Newbold, C.J., Roehe, Rainer, Dewhurst, Richard J., Snelling, Tim J., Watson, Mick, Suen, Garret, Hart, Elizabeth H., Kingston-Smith, Alison H., Scollan, Nigel D., Do Prado, Rodolpho M., Pilau, Eduardo J., Mantovani, Hilario C., Attwood, Graeme T., Edwards, Joan E., McEwan, Neil R., Morrisson, Steven, Mayorga, Olga L., Elliott, Christopher, Morgavi, Diego P., European Commission, Ministerio de Economía y Competitividad (España), Biotechnology and Biological Sciences Research Council (UK), Institute for Global Food Security [Belfast], Queen's University [Belfast] (QUB), Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev (BGU), Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Modélisation Systémique Appliquée aux Ruminants (MoSAR), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Animal and Grassland Research and Innovation Centre (AGRICE), College of Agricultural and Environmental Sciences, University of California [Davis] (UC Davis), University of California-University of California, Natural Resources Institute Finland (LUKE), Department of Agrotechnology and Food Sciences [Wageningen], Wageningen University and Research [Wageningen] (WUR), Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences (SLU), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Department of Agricultural, Food and Nutritional Science, University of Alberta, Lethbridge Research Centre, Agriculture and Agri-Food Canada, Scotland's Rural College (SRUC), The Rowett Institute, University of Aberdeen, The Roslin Institute and the Royal (Dick) School of Veterinary Studies (R(D)SVS), University of Edinburgh, Departments of Botany and Bacteriology, University of Wisconsin-Madison, Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Laboratório de Biomoléculas e Espectrometria de Massas-Labiomass, Departamento de Química, Universidade Estadual de Maringá, Universidade Federal de Viçosa (UFC), AgResearch Limited, School of Pharmacy and Life Sciences, Robert Gordon University (RGU), Sustainable Livestock, Agri-Food and Bio-Sciences Institute, Agri-Food and Biosciences Institute, Colombian Agricultural Research Corporation, European Project: 640384 ,RuMicroPlas, European Project: 706899,EQUIANFUN, Institute for Global Food Security, Department of Life Sciences and the National Institute for Biotechnology in the Negev, VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Animal and Bioscience Research Department, Irish Agriculture and Food Development Authority, Natural Resources Institute Finland, Department of Agrotechnology and Food Sciences, Wageningen University and Research Centre [Wageningen] (WUR), Estacion Experimental del Zaidin, Spanish National Research Council (CSIC), Lethbridge Research and Development Centre, Agriculture and Agri-Food [Ottawa] (AAFC), Scotland's Rural College (SCUR), Department of Microbiology, Nippon Dental University, Grasslands Research Centre, Laboratory of Microbiology, Northern Regional Institution of Hungarian National Public Health and Medical Officer Service, Robert Gordon University, Sustainable Livestock, Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Estación Experimental del Zaidín (EEZ), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), EU H2020 Marie Curie Fellowship 706899, European Project: 640384,H2020,ERC-2014-STG,RuMicroPlas(2016), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), University of California (UC)-University of California (UC), Agriculture and Agri-Food (AAFC), and Biotechnology and Biological Sciences Research Council (BBSRC)-Aberystwyth University
Subjects: Microbiology (medical), animal structures, Rumen, Environmental Science and Management, alimentation animale, [SDV]Life Sciences [q-bio], lcsh:QR1-502, microbiome, Omics, ruminant, Review, Microbiology, lcsh:Microbiology, modèle mathématique, Microbiologie, Genetics, VLAG, métagénomique, metagenomics, rumen, WIMEK, methane, Host, Human Genome, host, diet, production, omics, Production, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Diet, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Soil Sciences, biomarker, Zero Hunger, animal feeding, Microbiome, biomarqueur, Methane, mathematical model
Abstract: The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in >omic> data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent >omics> approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges., SH, DM, MP, RM-T, SW, IT, HS, JE, SK, GA, and CC acknowledge the support of ERA-net gas co-fund for funding (Project name: RumenPredict). SH, HM and CC acknowledge support from BBSRC (BBL/L026716/1 and BBL/L026716/2) and a British Council Newton Institutional Links funding (Grant 172629373). IM acknowledges funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant 640384). JE acknowledges funding from an EU H2020 Marie Curie Fellowship (706899). CC, AK-S, and EH were supported by the Biotechnology and Biological Sciences Research Council (Grants BBS/OS/GC/000011B and BBS/E/W/0012843D). CN and OM acknowledge the support of the British Council Newton Institutional Links funding (Grant 216425215). SRUC receives financial support from the Scottish Government's Rural and Environment Science and Analytical Services Division (RESAS). RD and RR acknowledge financial support from the Biotechnology and Biological Sciences Research Council (BBSRC BB/N01720X/1). DY-R and AB acknowledge funding from MINECO, Spain (Grant AGL2017-86938-R). GS acknowledges funding from the U.S. Department of Agriculture National Institute of Food and Agriculture foundational (Grant 2015-67015-23246). EP acknowledges funding from CNPq (Grant 401590/2014-3). All authors are also members of the Global Research Alliance Rumen Microbial Genomics network.
Published: 2018

33. Anti-infectious properties of the probiotic Saccharomyces cerevisiae CNCM I-3856 on enterotoxigenic E. coli (ETEC) strain H10407

Author: S Blanquet-Diot, S. Denis, Nathalie Ballet, Charlène Roussel, Adeline Sivignon, G Garrait, T. Van de Wiele, Varvara Tsilia, A de Vallée, Nicolas Barnich, Pascal Vandekerckove, Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Lesaffre Feed Additives (LFA), Roche Affiliate, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Université d'Auvergne - Clermont-Ferrand I (UdA), Ministere de la Recherche (France), Lesaffre Company (Marcq-en-Baroeul, France), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), and Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)
Subjects: 0301 basic medicine, Saccharomyces cerevisiae, Virulence, medicine.disease_cause, Probiotic, Applied Microbiology and Biotechnology, Microbiology, law.invention, 03 medical and health sciences, Mice, Enterotoxins, law, Enterotoxigenic Escherichia coli, Antibiosis, medicine, Animals, Humans, Escherichia coli, Escherichia coli Infections, Inflammation, biology, Probiotics, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, General Medicine, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Yeast, 3. Good health, Bacterial adhesin, 030104 developmental biology, Adhesion, Caco-2 Cells, Bacteria, Biotechnology
Abstract: International audience; Enterotoxigenic Escherichia coli (ETEC) are major food-borne pathogens responsible for traveler's diarrhea. The production of adhesins and the secretion of enterotoxins constitute the major virulence traits of the bacteria. Treatments are mainly symptomatic and can involve antibiotherapy. However, given the rise of antibiotic resistance worldwide, there is an urgent need for the development of new preventive strategies for the control of ETEC infections. Among them, a promising approach is the use of probiotics. The aim of this study was to investigate, using complementary in vitro and in vivo approaches, the inhibitory potential of the yeast Saccharomyces cerevisiae CNCM I-3856 against the human ETEC reference strain H10407. In conventional culture media, S. cerevisiae significantly reduced ETEC growth and toxin production. The yeast also inhibited bacterial adhesion to mucin-agar and intestinal Caco-2/TC7 cells in a dose-dependent manner. Lastly, pre-treatment with S. cerevisiae inhibited interleukin-8 production by ETEC-infected intestinal cells. In streptomycin-treated mice, the probiotic yeast decreased bacterial colonization, mainly in the ileum, the main site of ETEC pathogenesis. For the first time, this study shows that the probiotic yeast S. cerevisiae CNCM I-3856 can exert an anti-infectious activity against a human ETEC strain through a multi-targeted approach, including inhibition of bacterial growth and toxin production, reduction of bacterial adhesion to mucins and intestinal epithelial cells, and suppression of ETEC-induced inflammation. Interestingly, the highest activity was obtained with a prophylactic treatment. Further studies will aim to assess the effect of the yeast on ETEC survival and virulence under human simulated digestive conditions.
Published: 2018

34. Muscle fiber types identification by synchrotron fluorescence microspectroscopy

Author: Astruc, Thierry, Chagnot, Caroline, Venien, Annie, Jamme, Frederic, Refregiers, Mathieu, Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Synchrotron SOLEIL (SOLEIL), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), and Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix
Subjects: [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT], fibre musculaire, [SDV.BA]Life Sciences [q-bio]/Animal biology, skeletal myocytes, synchrotron, microspectroscopie, fluorescence
Abstract: The skeletal muscle consists of three to four pure types of muscle cells (also called muscle fibers) identified as type I, type IIA, type IIX and/or type IIB in different proportions depending on the muscle function. They differ in their contraction speeds and metabolic pathways. Type I fibers are slow-twitch while type II fibers are fast twitch. The energy required to maintain cell homeostasis and muscle contraction is provided by the hydrolysis of ATP. The fibers IIX and IIB regenerate ATP by anaerobic glycolysis with lactate production. Fibers I and IIA favor cellular respiration (glycolysis + Krebs cycle). The latter are rich in mitochondria, where the cell respiration take place, and in myoglobin which carries oxygen to mitochondria. The intracellular composition of fibers therefore depends on their metabolic and contractile characteristics. The objective of our work was to study the impact of these slight differences in composition on the optical properties of muscle cells. Our hypothesis was, in part, based on the autofluorescence detection of NADH which is more concentrated in the mitochondria and thus in the oxidative metabolism fibers. Therefore, we studied the impact of cell type on the fluorescent response following excitation in deep UV. Rat soleus muscle consisting of I and IIA fibers and extensor digitorum longus (EDL) muscle consisting of I, IIA, IIX and IIB fibers were used as models. On each muscle, fibers, previously identified on their cell types by immunohistofluorescence, were analyzed by synchrotron fluorescence microspectroscopy on stain-free serial muscle cross sections. Muscle fibers excited at 275 nm showed differences in fluorescence emission intensity among fiber types at 302 (assigned to tyrosine fluorescence), 325, 346 (both assigned to tryptophan fluorescence) and 410 nm (assigned to NADH fluorescence). The 410/325 ratio decreased significantly with contractile and metabolic features in EDL muscle, ranked I>IIA>IIX>IIB fibers (p< 0.01). In a subsequent experiment, we acquired autofluorescence images for fast fiber types discrimination on label free histological sections. Computer processing of the images allowed us to improve the contrast and identify the metabolic types of fibers with a fairly good reliability. These studies highlight the usefulness of autofluorescence signals to characterize histological cross section of muscle fibers with no staining chemicals.
Published: 2018

35. Identification of the Autochaperone Domain in the Type Va Secretion System (T5aSS): Prevalent Feature of Autotransporters with a β-Helical Passenger

Author: Maricarmen Rojas-Lopez, Mohamed A. Zorgani, Lawrence A. Kelley, Xavier Bailly, Andrey V. Kajava, Ian R. Henderson, Fabio Polticelli, Mariagrazia Pizza, Roberto Rosini, Mickaël Desvaux, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), INRA, UR346 Epidémiologie Animale, Institut National de la Recherche Agronomique (INRA), Centre de recherche en Biologie Cellulaire (CRBM), Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1), Institute of Microbiology and Infection, University of Birmingham [Birmingham], Dipartimento di Biologia, Roma Tre University, GlaxoSmithKline [Siena, Italy] (GSK), Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Structural Bioinformatics Group, Imperial College London, Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Centre de recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi Roma Tre = Roma Tre University (ROMA TRE), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 2 - Sciences et Techniques (UM2), Rojas-Lopez, Maricarmen, Zorgani, Mohamed A., Kelley, Lawrence A., Bailly, Xavier, Kajava, Andrey V., Henderson, Ian R., Polticelli, Fabio, Pizza, Mariagrazia, Rosini, Roberto, Desvaux, Mickaël, and Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Microbiology (medical), autochaperone domain, Sequence analysis, Structural alignment, lcsh:QR1-502, translocation, Virulence, protein secretion system, autotransporters, Type V secretion system, outer membrane protein, protein translocation, diderm-LPS Gram-negative bacteria, Computational biology, Biology, Outer membrane proteins, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Hydrolase, Secretion, ComputingMilieux_MISCELLANEOUS, Original Research, Protein translocation, 030102 biochemistry & molecular biology, sécrétion protéique, Autochaperone domain, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 030104 developmental biology, Secretory protein, Autotransporter, Diderm-LPS Gram-negative bacteria, Outer membrane protein, Protein secretion system, Bacterial outer membrane, protéine de la membrane externe, Autotransporters
Abstract: International audience; Autotransporters (ATs) belong to a family of modular proteins secreted by the Type V, subtype a, secretion system (T5aSS) and considered as an important source of virulence factors in lipopolysaccharidic diderm bacteria (archetypical Gram-negative bacteria). While exported by the Sec pathway, the ATs are further secreted across the outer membrane via their own C-terminal translocator forming a b-barrel, through which the rest of the protein, namely the passenger, can pass. In several ATs, an autochaperone domain (AC) present at the C-terminal region of the passenger and upstream of the translocator was demonstrated as strictly required for proper secretion and folding. However, considering it was functionally characterised and identified only in a handful of ATs, wariness recently fells on the commonality and conservation of this structural element in the T5aSS. To circumvent the issue of sequence divergence and taking advantage of the resolved three-dimensional structure of some ACs, identification of this domain was performed following structural alignment among all AT passengers experimentally resolved by crystallography before searching in a dataset of 1523 ATs. While demonstrating that the AC is indeed a conserved structure found in numerous ATs, phylogenetic analysis further revealed a distribution into deeply rooted branches, from which emerge 20 main clusters. Sequence analysis revealed that an AC could be identified in the large majority of SAATs (self-associating ATs) but not in any LEATs (lipase/esterase ATs) nor in some PATs (protease autotransporters) and PHATs (phosphatase/hydrolase ATs). Structural analysis indicated that an AC was present in passengers exhibiting single-stranded right-handed parallel b-helix, whatever the type of b-solenoid, but not with a-helical globular fold. From this investigation, the AC of type 1 appears as a prevalent and conserved structural element exclusively associated to b-helical AT passenger and should promote further studies about the protein secretion and folding via the T5aSS, especially toward a-helical AT passengers.
Published: 2018

36. Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis

Author: Sylvain Charlat, Pierre Peyret, Marie Cariou, Jean-Christophe Simon, Jean-Pierre Gauthier, Céline Ribière, Stéphanie Morlière, Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Namur [Namur] (UNamur), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), CapSymbArt, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Namur [Namur], Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, 16S, 030106 microbiology, lcsh:Medicine, Computational biology, DNA, Ribosomal, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, law.invention, 03 medical and health sciences, microbiote, law, RNA, Ribosomal, 16S, Animals, Pea aphid, lcsh:Science (General), lcsh:QH301-705.5, Ribosomal DNA, Polymerase chain reaction, diversité, Amplicon sequencing, biology, DNA–DNA hybridization, Microbiota, lcsh:R, Peas, High-Throughput Nucleotide Sequencing, food and beverages, General Medicine, Sequence Analysis, DNA, Amplicon, biology.organism_classification, 16S ribosomal RNA, Acyrthosiphon pisum, Research Note, 030104 developmental biology, Hybridization capture, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, lcsh:Biology (General), Metagenomics, puceron, Aphids, séquençage adn, hybridation, lcsh:Q1-390, hybridization capture, amplicon sequencing, pea aphid, microbiota
Abstract: Objective Targeted sequencing of 16S rDNA amplicons is routinely used for microbial community profiling but this method suffers several limitations such as bias affinity of universal primers and short read size. Gene capture by hybridization represents a promising alternative. Here we used a metagenomic extract from the pea aphid Acyrthosiphon pisum to compare the performances of two widely used PCR primer pairs with DNA capture, based on solution hybrid selection. Results All methods produced an exhaustive description of the 8 bacterial taxa known to be present in this sample. In addition, the methods yielded similar quantitative results, with the number of reads strongly correlating with quantitative PCR controls. Both methods can thus be considered as qualitatively and quantitatively robust on such a sample with low microbial complexity. Electronic supplementary material The online version of this article (10.1186/s13104-018-3559-3) contains supplementary material, which is available to authorized users.
Published: 2018

37. Characterisation of gut, lung, and upper airways microbiota in patients with non-small cell lung carcinoma Study protocol for case-control observational trial Study Protocol Clinical Trial

Author: Bingula, Rea, Filaire, Marc, Radosevic-Robin, Nina, Berthon, Jean-Yves, Bernalier-Donadille, Annick, VASSON, Marie-Paule, Thivat, Emilie, Kwiatkowski, Fabrice, Filaire, Edith, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Centre Jean Perrin, CRLCC Jean Perrin, Biopôle Clermont-Limagne, GREENTECH, Microbiologie Equipe Qualité et Sécurité des Aliments (INRA), Institut National de la Recherche Agronomique (INRA), Imagerie Moléculaire et Stratégies Théranostiques - Clermont Auvergne (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER, Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), SECurité des ALIments et Microbiologie, Institut National de la Recherche Agronomique (INRA)-École nationale d'ingénieurs des techniques des industries agricoles et alimentaires (ENITIAA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: gut-lung axis, microbiota, [SDV.CAN]Life Sciences [q-bio]/Cancer, tumour microenvironment, chemotherapy, non-small cell lung cancer, immune response, respiratory tract diseases
Abstract: International audience; Background: Several studies have confirmed the important role of the gut microbiota in the regulation of immune functions and its correlation with different diseases, including cancer. While brain-gut and liver-gut axes have already been demonstrated, the existence of a lung-gut axis has been suggested more recently, with the idea that changes in the gut microbiota could affect the lung microbiota, and vice versa. Likewise, the close connection between gut microbiota and cancer of proximal sites (intestines, kidneys, liver, etc.) is already well established. However, little is known whether there is a similar relation when looking at world's number one cause of death from cancer-lung cancer. Objective: Firstly, this study aims to characterise the gut, lung, and upper airways (UAs) microbiota in patients with non-small cell lung cancer (NSCLC) treated with surgery or neoadjuvant chemotherapy plus surgery. Secondly, it aims to evaluate a chemotherapy effect on site-specific microbiota and its influence on immune profile. To our knowledge, this is the 1st study that will analyse multi-site microbiota in NSCLC patients along with site-specific immune response. Methods: The study is a case-controlled observational trial. Forty NSCLC patients will be divided into 2 groups depending on their anamnesis: Pchir, patients eligible for surgery, or Pct-chir, patients eligible for neoadjuvant chemotherapy plus surgery. Composition of the UAs (saliva), gut (faeces), and lung microbiota (from broncho-alveolar lavage fluid (BALF) and 3 lung pieces: "healthy" tissue distal to tumour, peritumoural tissue and tumour itself) will be analysed in both groups. Immune properties will be evaluated on the local (evaluation of the tumour immune cell infiltrate, tumour classification and properties, immune cell phenotyping in BALF; human neutrophil protein (HNP) 1-3, b-defensin 2, and calprotectin in faeces) and systemic level (blood cytokine and immune cell profile). Short-chain fatty acids (SCFAs) (major products of bacterial fermentation with an effect on immune system) will be dosed in faecal samples. Other factors such as nutrition and smoking status will be recorded for each patient. We hypothesise that smoking status and tumour type/grade will be major factors influencing both microbiota and immune/inflammatory profile of all sampling sites. Furthermore, due to non-selectivity, the same effect is expected from chemotherapy. Abbreviations: ANSM = The French National Agency for Medicines and Health Products Safety (Agence nationale de sécurité du médicament et des produits de santé), BAL = broncho-alveolar lavage, BALF = broncho-alveolar lavage fluid, BMI = body mass index, CIFRE = Industrial Research Training Agreements grant (Convention industrielle de formation par la recherché), CRP = C-reactive protein, CT = chemotherapy, ELISA = enzyme-linked immunosorbent assay, FDR = false discovery rate, GF = germ-free, GI = gastrointestinal, HBSS = Hank's balanced salt solution, HNP = human neutrophil peptide, ICI = immune checkpoint inhibitor, IL = interleukin, MCLB = mammalian cell lysis buffer, NSCLC = non-small cell lung cancer, OTU = outer taxonomic unit, Pchir = patient surgery, fr. «patient chirurgie», Pct-chir = patients chemotherapy plus surgery, fr. «patient chimiothérapie-chirurgie», qPCR = quantitative polymerase chain reaction, SCFAs = short-chain fatty acids, UAs = upper airways.
Published: 2018

38. Food chemicals disrupt human gut microbiota activity and impact intestinal homeostasis as revealed by in vitro systems

Author: Defois, Clémence, Ratel, Jérémy, Garrait, Ghislain, Denis, Sylvain, Le Goff, Olivier, Talvas, Jeremie, Mosoni, Pascale, Engel, Erwan, Peyret, Pierre, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Ministere de l'Enseignement Superieur et de la Recherche of France, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), and INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA)
Subjects: produit chimique, [SDV]Life Sciences [q-bio], lcsh:R, lcsh:Medicine, chemicals, Epithelial Cells, Food Contamination, in vitro, Gene Expression Regulation, Bacterial, digestive system, Article, Cell Line, Gastrointestinal Microbiome, Xenobiotics, Intestines, homeostasis, microflore digestive, Humans, lcsh:Q, Environmental Pollutants, lcsh:Science, Transcriptome, homéostasie
Abstract: Growing evidence indicates that the human gut microbiota interacts with xenobiotics, including persistent organic pollutants and foodborne chemicals. The toxicological relevance of the gut microbiota-pollutant interplay is of great concern since chemicals may disrupt gut microbiota functions, with a potential impairment of host homeostasis. Herein we report within batch fermentation systems the impact of food contaminants (polycyclic aromatic hydrocarbons, polychlorobiphenyls, brominated flame retardants, dioxins, pesticides and heterocyclic amines) on the human gut microbiota by metatranscriptome and volatolome i.e. “volatile organic compounds” analyses. Inflammatory host cell response caused by microbial metabolites following the pollutants-gut microbiota interaction, was evaluated on intestinal epithelial TC7 cells. Changes in the volatolome pattern analyzed via solid-phase microextraction coupled to gas chromatography-mass spectrometry mainly resulted in an imbalance in sulfur, phenolic and ester compounds. An increase in microbial gene expression related to lipid metabolism processes as well as the plasma membrane, periplasmic space, protein kinase activity and receptor activity was observed following dioxin, brominated flame retardant and heterocyclic amine exposure. Conversely, all food contaminants tested induced a decreased in microbial transcript levels related to ribosome, translation and nucleic acid binding. Finally, we demonstrated that gut microbiota metabolites resulting from pollutant disturbances may promote the establishment of a pro-inflammatory state in the gut, as stated with the release of cytokine IL-8 by intestinal epithelial cells.
Published: 2018

39. Surfaceome and Proteosurfaceome in Parietal Monoderm Bacteria: Focus on Protein Cell-Surface Display

Author: Desvaux, Mickael, Candela, Thomas, Serror, Pascale, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Bactéries, Pathogènes et Santé (UBaPS), Faculté de Pharmacie, Université Paris-Sud - Paris 11 (UP11)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11)-Université Paris-Saclay, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, INRA (Institut National de la Recherche Agronomique), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université Paris-Sud - Paris 11 (UP11)-Université Paris-Sud - Paris 11 (UP11), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])
Subjects: surface cellulaire, lcsh:QR1-502, surface proteins, membrane proteins, Review, Microbiology, lcsh:Microbiology, LPXTG sortase-dependent protein, subcellular localization, membrane protein, lipoprotéines, Microbiology and Parasitology, lipoprotein, surfaceome, pili/fimbriae/curli, Microbiologie et Parasitologie, gram-positive bacteria, cell-surface protein, surface proteome, gram positive bacteria, lipoproteins, LPXTG sortase-dependent proteins, cell surface, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, protéine membranaire, bactérie gram positif
Abstract: The cell envelope of parietal monoderm bacteria (archetypal Gram-positive bacteria) is formed of a cytoplasmic membrane (CM) and a cell wall (CW). While the CM is composed of phospholipids, the CW is composed at least of peptidoglycan (PG) covalently linked to other biopolymers, such as teichoic acids, polysaccharides, and/or polyglutamate. Considering the CW is a porous structure with low selective permeability contrary to the CM, the bacterial cell surface hugs the molecular figure of the CW components as a well of the external side of the CM. While the surfaceome corresponds to the totality of the molecules found at the bacterial cell surface, the proteinaceous complement of the surfaceome is the proteosurfaceome. Once translocated across the CM, secreted proteins can either be released in the extracellular milieu or exposed at the cell surface by associating to the CM or the CW. Following the gene ontology (GO) for cellular components, cell-surface proteins at the CM can either be integral (GO: 0031226), i.e., the integral membrane proteins, or anchored to the membrane (GO: 0046658), i.e., the lipoproteins. At the CW (GO: 0009275), cell-surface proteins can be covalently bound, i.e., the LPXTG-proteins, or bound through weak interactions to the PG or wall polysaccharides, i.e., the cell wall binding proteins. Besides monopolypeptides, some proteins can associate to each other to form supramolecular protein structures of high molecular weight, namely the S-layer, pili, flagella, and cellulosomes. After reviewing the cell envelope components and the different molecular mechanisms involved in protein attachment to the cell envelope, perspectives in investigating the proteosurfaceome in parietal monoderm bacteria are further discussed.
Published: 2018

40. MALDI mass spectrometry imaging and in situ microproteomics of Listeria monocytogenes biofilms

Author: Delphine Centeno, Tiago Santos, Michel Hébraud, Laetitia Théron, Julia Esbelin, Christophe Chambon, Didier Viala, Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Unité de Nutrition Humaine (UNH), European Union 641984, European Project: 641984,H2020,H2020-MSCA-ITN-2014,List_MAPS(2015), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Unité de Nutrition Humaine - Clermont Auvergne (UNH), and Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA)
Subjects: Proteomics, 0301 basic medicine, MALDI imaging, Proteome, Food Handling, Microorganism, [SDV]Life Sciences [q-bio], Food spoilage, Biophysics, Food Contamination, medicine.disease_cause, Biochemistry, Mass spectrometry imaging, biofilm, 03 medical and health sciences, stress, Bacterial Proteins, Listeria monocytogenes, Stress, Physiological, Tandem Mass Spectrometry, medicine, Food science, Desiccation, dehumidification stress, LC-MS/MS, MALDI, dehumidification, 2. Zero hunger, biology, Chemistry, Biofilm, déshumidification, biology.organism_classification, 030104 developmental biology, 13. Climate action, Biofilms, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Food Microbiology, MALDI MSI, listeria monocytogènes, Bacteria, Chromatography, Liquid
Abstract: Epub 2018 Jul 30; MALDI-TOF Mass spectrometry Imaging (MSI) is a surface-sampling technology that can determine spatial information and relative abundance of analytes directly from biological samples. Human listeriosis cases are due to the ingestion of contaminated foods with the pathogenic bacteria Listeria monocytogenes. The reduction of water availability in food workshops by decreasing the air relative humidity (RH) is one strategy to improve the control of bacterial contamination. This study aims to develop and implement an MSI approach on L. monocytogenes biofilms and proof of concept using a dehumidified stress condition. MSI allowed examining the distribution of low molecular weight proteins within the biofilms subjected to a dehumidification environment, mimicking the one present in a food workshop (10 °C, 75% RH). Furthermore, a LC-MS/MS approach was made to link the dots between MSI and protein identification. Five identified proteins were assigned to registered MSI m/z, including two cold-shock proteins and a ligase involved in cell wall biogenesis. These data demonstrate how imaging can be used to dissect the proteome of an intact bacterial biofilm giving new insights into protein expression relating to a dehumidification stress adaptation. Data are available via ProteomeXchange with identifier PXD010444.BIOLOGICAL SIGNIFICANCE:The ready-to-eat food processing industry has the daily challenge of controlling the contamination of surfaces and machines with spoilage and pathogenic microorganisms. In some cases, it is a lost cause due to these microorganisms' capacity to withstand the cleaning treatments, like desiccation procedures. Such a case is the ubiquitous Gram-positive Bacterium Listeria monocytogenes. Its surface proteins have particular importance for the interaction with its environment, being important factors contributing to adaptation to stress conditions. There are few reproducibly techniques to obtain the surface proteins of Gram-positive cells. Here, we developed a workflow that enables the use of MALDI imaging on Gram-positive bacterium biofilms to study the impact of dehumidification on sessile cells. It will be of the most interest to test this workflow with different environmental conditions and potentially apply it to other biofilm-forming bacteria.
Published: 2018

41. Development of a Mass Spectrometry Imaging (MSI) approach to explore Listeria monocytogenes biofilms exposed to a dehumidification stress

Author: Santos, Tiago, Theron, Laetitia, Chambon, Christophe, Viala, Didier, Centeno, Delphine, Hébraud, Michel, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: microorganisme, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, spectrométrie de masse, Microbiology and Parasitology, mass spectrum analysis, déshumidification, biochemical phenomena, metabolism, and nutrition, listeria monocytogènes, Microbiologie et Parasitologie, digestive system diseases, biofilm, dehumidification
Abstract: Development of a Mass Spectrometry Imaging (MSI) approach to explore Listeria monocytogenes biofilms exposed to a dehumidification stress. 8. Colloque du Réseau National Biofilms
Published: 2017

42. Biofilms de Listeria monocytogenes soumis à une diminution de l’humidité relative de l’air

Author: Esbelin, Julia, Mille, Thomas, Gaillard-Martinie, Brigitte, Viala, Didier, Chambon, Christophe, Hébraud, Michel, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), ProdInra, Archive Ouverte, Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), and Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement
Subjects: microorganisme, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, humidité relative de l'air, Microbiology and Parasitology, déshumidification, biochemical phenomena, metabolism, and nutrition, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, listeria monocytogènes, ComputingMilieux_MISCELLANEOUS, Microbiologie et Parasitologie, biofilm
Abstract: Biofilms de Listeria monocytogenes soumis à une diminution de l’humidité relative de l’air. 8. Colloque du Réseau National Biofilms
Published: 2017

43. MALDI imaging and profiling mass spectrometry approach for the analysis of Listeria monocytogenes biofilms exposed to a desiccation

Author: Santos, Tiago, Theron, Laetitia, Chambon, Christophe, Viala, Didier, Centeno, Delphine, Hébraud, Michel, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, spectrométrie de masse, Microbiology and Parasitology, mass spectrum analysis, listeria monocytogènes, Microbiologie et Parasitologie, biofilm, matrix assisted laser desorption ionization, maldi
Abstract: MALDI imaging and profiling mass spectrometry approach for the analysis of Listeria monocytogenes biofilms exposed to a desiccation. SMMAP 2017, Spectrométrie de Masse, Métabolomique et Analyse Protéomique
Published: 2017

44. Development of a MALDI imaging mass spectrometry (IMS) approach to bacterial proteomics: first application to Listeria monocytogenes biofilms exposed to a desiccation

Author: Santos, Tiago, Theron, Laetitia, Centeno, Delphine, Chambon, Christophe, Viala, Didier, Hébraud, Michel, Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Unité Mixte de Recherches sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, and Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix
Subjects: proteomics, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, spectrométrie de masse, Microbiology and Parasitology, mass spectrum analysis, protéomique, listeria monocytogènes, Microbiologie et Parasitologie, biofilm
Abstract: Development of a MALDI imaging mass spectrometry (IMS) approach to bacterial proteomics: first application to Listeria monocytogenes biofilms exposed to a desiccation. 7. Congress of European Microbiologists FEMS 2017
Published: 2017

45. Colonic transit time is a driven force of the gut microbiota composition and metabolism: In vitro evidence

Author: Benoit Sion, William Tottey, David Feria-Gervasio, Jean-François Martin, Jean-Louis Sébédio, Nadia Gaci, Jean-François Jarrige, Monique Alric, Jean-François Brugère, Estelle Pujos, Brigitte Laillet, EA 4678, Faculté de Pharmacie, Université d'Auvergne - Clermont-Ferrand I (UdA), Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Unité de recherche sur les Biopolymères, Interactions Assemblages (BIA), Institut National de la Recherche Agronomique (INRA), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Auvergne Council (FEDER), Conception, Ingénierie et Développement de l'Aliment et du Médicament ( CIDAM ), Université d'Auvergne - Clermont-Ferrand I ( UdA ), Microbiologie Environnement Digestif Santé - Clermont Auvergne ( MEDIS ), Université Clermont Auvergne ( UCA ) -INRA Clermont-Ferrand-Theix, Unité Mixte de Recherches sur les Herbivores ( UMR 1213 Herbivores ), VetAgro Sup ( VAS ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ), Unité de Nutrition Humaine ( UNH ), Clermont Université-Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Institut National de la Recherche Agronomique ( INRA ), Neuro-Dol - Clermont Auvergne ( Neuro-Dol ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Université Clermont Auvergne ( UCA ), Institut de France, Université d'Auvergne (Clermont Ferrand 1) (UdA), Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Brugère, Jean François, INRA Clermont-Ferrand-Theix-Université Clermont Auvergne ( UCA ), and Institut National de la Recherche Agronomique ( INRA ) -Université d'Auvergne - Clermont-Ferrand I ( UdA ) -Clermont Université
Subjects: 0301 basic medicine, Metabolite, Population, Médecine humaine et pathologie, gut microbiome, Chemostat, Gut flora, digestive system, personne âgée, 03 medical and health sciences, chemistry.chemical_compound, flore intestinale, Carbohydrate fermentation, Food and Nutrition, aging, colon, constipation, microbiological techniques, education, ComputingMilieux_MISCELLANEOUS, senior citizens, education.field_of_study, biology, [ SDV ] Life Sciences [q-bio], Short-chain fatty acid, digestive, oral, and skin physiology, Gastroenterology, Metabolism, biology.organism_classification, In vitro, 030104 developmental biology, chemistry, Biochemistry, Alimentation et Nutrition, Human health and pathology, Original Article, Neurology (clinical), durée du transit, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract: Jean-François Brugère thanks bachelors’students for their help, more specifically Céline Vidal, Claire Ardaens,Adeline Régnier, and Amandine Maurin, and Sylvain Denis forhis valuable help concerning in vitro systems. In memory of GeorgeT MacFarlane (died in 2015) for all of his pioneering works on gut in vitro simulations systemsThis work was supported by the European Union (UE) through the Auvergne Council (FEDER) with a PhD and a postdoctoral Scholarship support respectively to William Tottey and to David Feria-Gervasio, and by a PhD scholarship support from the French "Ministere de l'Enseignement Superieur et de la Recherche" to Nadia Gaci; Background/Aims: Human gut microbiota harbors numerous metabolic properties essential for the host's health. Increased intestinal transit time affects a part of the population and is notably observed with human aging, which also corresponds to modifications of the gut microbiota. Thus we tested the metabolic and compositional changes of a human gut microbiota induced by an increased transit time simulated in vitro. Methods: The in vitro system, Environmental Control System for Intestinal Microbiota, was used to simulate the environmental conditions of 3 different anatomical parts of the human colon in a continuous process. The retention times of the chemostat conditions were established to correspond to a typical transit time of 48 hours next increased to 96 hours. The bacterial communities, short chain fatty acids and metabolite fingerprints were determined. Results: Increase of transit time resulted in a decrease of biomass and of diversity in the more distal compartments. Short chain fatty acid analyses and metabolite fingerprinting revealed increased activity corresponding to carbohydrate fermentation in the proximal compartments while protein fermentations were increased in the lower parts. Conclusions: This study provides the evidence that the increase of transit time, independently of other factors, affects the composition and metabolism of the gut microbiota. The transit time is one of the factors that explain some of the modifications seen in the gut microbiota of the elderly, as well as patients with slow transit time.
Published: 2017

46. Colonisation of meat by escherichia coli O157:H7: Investigating bacterial tropism with respect to the different types of skeletal mMuscles, Subtypes of mMyofibres, and postmortem time

Author: Chagnot, Caroline, Venien, Annie, Renier, Sandra, Caccia, Nelly, Talon, Régine, Astruc, Thierry, Desvaux, Mickael, Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Qualité des Produits Animaux (QuaPA), Institut National de la Recherche Agronomique (INRA), INRA ('Institut national de la Recherche Agronomique'), MICel ('Mecanismes moleculaires impliques dans l'interaction entre bacteries et cellules musculaires') project - inter-department, CEPIA/MICA ('Caracterisation et Elaboration des Produits Issus de l'Agriculture/Microbiologie et Chaine Alimentaire'), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), and Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix
Subjects: contamination alimentaire, foodborne pathogen, extracellular matrix, adhésion bactérienne, matrice extracellulaire, muscle squelettique, bacterial adhesion, voluntary muscle, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, food contamination, meat product, escherichia coli, pathogen, agent pathogène
Abstract: Escherichia coli O157:H7 is an enterohaemorrhagic E. coli (EHEC) responsible for serious diseases, especially pediatric, and of great concern for the meat industry.Meat contamination by EHEC occurs at slaughtering, especially at dehiding stage, where bacteria can be transferred from hides to carcasses. The skeletal muscle tissues comprise four major types of myofibres, which differ in their contraction velocity and metabolism. Myofibres are surrounded by the extracellular matrix (ECM). Adhesion of E. coli O157:H7 to meat was investigated considering well-defined types of skeletal muscle and their constituent myofibres as well as postmortem changes in muscle, using fluorescence microscopy and immunohistochemical analyses. By analysing the adhesion of E. coli O157:H7 to model oxidative (soleus) and glycolytic [extensor digitorum longus (EDL)] skeletal muscles, it first appeared that differential adhesion occurred at the surface of these extreme skeletal muscle types. At a cellular level, bacterial adhesion appeared to occur essentially at the ECM. Considering the different constituent myofibres of types I, IIA, IIX and IIB, no significant differences were observed for adhering bacteria. However, bacterial adhesion to the ECM was significantly influenced by postmortem structural modifications of muscle tissues. By providing information on spatial localisation of E. coli O157:H7 on meat, this investigation clearly demonstrated their ability to adhere to skeletal muscle, especially at the ECM, which consequently resulted in their heterogeneous distribution in meat. As discussed, these new findings should help in reassessing and mitigating the risk of contamination of meat, the food chain and ultimately human infection by EHEC.
Published: 2017

47. Foodborne enterotoxigenic Escherichia coli: from gut pathogenesis to new preventive strategies involving probiotics

Author: Adeline Sivignon, Tom Van de Wiele, Charlène Roussel, Stéphanie Blanquet-Diot, CRNH, Développement de l'Aliment et du Médicament, Université d'Auvergne (Clermont Ferrand 1) (UdA), Center for Microbial Ecology and Technology, Ghent University [Belgium] (UGENT), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte - Clermont Auvergne (M2iSH), Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne), Lesaffre Company (Marcq-en-Baroeul, France), Université d'Auvergne - Clermont-Ferrand I (UdA), Center for Microbial Ecology and Technology (CMET), Universiteit Gent = Ghent University [Belgium] (UGENT), Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)-Institut National de la Recherche Agronomique (INRA), Universiteit Gent = Ghent University (UGENT), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), and Institut National de la Recherche Agronomique (INRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre de Recherche en Nutrition Humaine d'Auvergne (CRNH d'Auvergne)
Subjects: 0301 basic medicine, pig, Gastrointestinal Diseases, virulence factors, medicine.disease_cause, in vitro digestion models, law.invention, Pathogenesis, Foodborne Diseases, Probiotic, law, Enterotoxigenic Escherichia coli, vaccine, ST/LT toxins, pathogénèse, Escherichia coli Infections, gastrointestinal cues, pathogenesis, Hydrogen-Ion Concentration, probiotique, 3. Good health, prévention, Diarrhea, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, medicine.symptom, escherichia coli, strategy, probiotic, Microbiology (medical), foodborne pathogen, 030106 microbiology, Virulence, Biology, nutritional strategies, Microbiology, 03 medical and health sciences, Antibiotic resistance, medicine, Humans, Mode of action, Escherichia coli, stratégie, ETEC, mortalité infantile, Gastrointestinal Microbiome, Gastrointestinal Tract, 030104 developmental biology, probiotics, Immunology
Abstract: Enterotoxigenic Escherichia coli (ETEC) are a major cause of traveler's diarrhea and infant mortality in developing countries. Given the rise of antibiotic resistance worldwide, there is an urgent need for the development of new preventive strategies. Among them, a promising approach is the use of probiotics. Although many studies, mostly performed under piglet digestive conditions, have shown the beneficial effects of probiotics on ETEC by interfering with their survival, virulence or adhesion to mucosa, underlying mechanisms remain unclear. This review describes ETEC pathogenesis, its modulation by human gastrointestinal cues as well as novel preventive strategies with a particular emphasis on probiotics. The potential of in vitro models simulating human digestion in elucidating probiotic mode of action will be discussed.
Published: 2017

48. Desired turbulence? Gut-lung axis, immunity, and lung cancer

Author: Bingula, Rea, Filaire, Marc, Radosevic-Robin, Nina, Bey, Mathieu, Berthon, Jean-Yves, Bernalier-Donadille, Annick, Vasson, Marie-Paule, Filaire, Edith, Microbiologie Environnement Digestif Santé (MEDIS), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Unité de Nutrition Humaine (UNH), Comprehensive Cancer Centre,Thoracic Surgery Unit, Centre Jean Perrin [Clermont-Ferrand] (UNICANCER/CJP), UNICANCER-UNICANCER, Comprehensive Cancer Centre, Department of Pathology, Imagerie Moléculaire et Stratégies Théranostiques (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Biopôle Clermont-Limagne, GREENTECH, Comprehensive Cancer Centre, University Clinic Würzburg, Complexité, Innovation, Activités Motrices et Sportives (CIAMS), Université Paris-Sud - Paris 11 (UP11)-Université d'Orléans (UO), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Unité de Nutrition Humaine - Clermont Auvergne (UNH), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne (UCA), Centre Jean Perrin - Centre Régional de Lutte contre le Cancer d'Auvergne, Imagerie Moléculaire et Stratégies Théranostiques - Clermont Auvergne (IMoST), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA), Université d'Orléans (UO)-Université Paris-Sud - Paris 11 (UP11), ProdInra, Archive Ouverte, and INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA)
Subjects: Article Subject, système immunitaire, Microbiology and Parasitology, [SDV.CAN]Life Sciences [q-bio]/Cancer, Review Article, lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens, lcsh:RC254-282, Microbiologie et Parasitologie, lung cancer, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.CAN] Life Sciences [q-bio]/Cancer, microbiote, intestin, cancer du poumon, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, intestine, Cancer
Abstract: The microbiota includes different microorganisms consisting of bacteria, fungi, viruses, and protozoa distributed over many human body surfaces including the skin, vagina, gut, and airways, with the highest density found in the intestine. The gut microbiota strongly influences our metabolic, endocrine, and immune systems, as well as both the peripheral and central nervous systems. Recently, a dialogue between the gut and lung microbiota has been discovered, suggesting that changes in one compartment could impact the other compartment, whether in relation to microbial composition or function. Further, this bidirectional axis is evidenced in an, either beneficial or malignant, altered immune response in one compartment following changes in the other compartment. Stimulation of the immune system arises from the microbial cells themselves, but also from their metabolites. It can be either direct or mediated by stimulated immune cells in one site impacting the other site. Additionally, this interaction may lead to immunological boost, assisting the innate immune system in its antitumour response. Thus, this review offers an insight into the composition of these sites, the gut and the lung, their role in shaping the immune system, and, finally, their role in the response to lung cancer.
Published: 2017

49. Effect of landscape features on the relationship between Ixodes ricinus ticks and their small mammal hosts

Author: Frédéric Faille, Grégoire Perez, Olivier Plantard, Axelle Durand, Yann Rantier, Suzanne Bastian, Albert Agoulon, Agnès Bouju, Isabelle Lebert, Alain Butet, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), UMR 1300 Biologie, Epidémiologie et Analyse du Risque, Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Biologie, Epidémiologie et Analyse du Risque (BioEpAR)-Santé animale (S.A.), Biologie, Epidémiologie et analyse de risque en Santé Animale (BIOEPAR), Institut National de la Recherche Agronomique (INRA), Unité de Microbiologie CR INRA Clermont Ferrand (UNITé DE MICROBIOLOGIE), ANR-11- Agro-001-04, Agence Nationale de la Recherche, Conseil Régional de Bretagne, ANR-11-AGRO-0001,OSCAR,Outil de Simulation Cartographique à l'échelle du paysage Agricole du Risque acarologique(2011), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Perez, Grégoire, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), and Unité de Microbiologie (MIC)
Subjects: 0106 biological sciences, 0301 basic medicine, Male, Apodemus sylvaticus, Ixodes ricinus, Woodland, Forests, 01 natural sciences, Mice, Abundance (ecology), Myodes glareolus, Ecotone, Mammals, biology, Agricultural landscape, Ecology, Arvicolinae, Bank vole, Infectious Diseases, Tick-Borne Diseases, Larva, [SDE]Environmental Sciences, Female, France, Nymph, Farms, [SDE.MCG]Environmental Sciences/Global Changes, 030106 microbiology, Tick, 010603 evolutionary biology, 03 medical and health sciences, parasitic diseases, Animals, Ecosystem, Host-parasite system, Ixodes, Research, fungi, 15. Life on land, biology.organism_classification, Insect Vectors, Tick Infestations, Wood mouse, Forest landscapes, 13. Climate action, Parasitology, Murinae, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Landscape connectivity
Abstract: International audience; Background: The consequences of land use changes are among the most cited causes of emerging infectious diseases because they can modify the ecology and transmission of pathogens. This is particularly true for vector-borne diseases which depend on abiotic (e.g. climate) and biotic conditions (i.e. hosts and vectors). In this study, we investigated how landscape features affect the abundances of small mammals and Ixodes ricinus ticks, and how they influence their relationship. Methods: From 2012 to 2014, small mammals and questing I. ricinus ticks were sampled in spring and autumn in 24 sites located in agricultural and forest landscapes in Brittany, France. We tested the effects of landscape features (composition and configuration) on the abundances of small mammal species and immature ticks and their relationship. Additionally, we quantified the larval tick burden of small mammals in 2012 to better describe this relationship. Results: The nymph abundance was positively influenced by the larval occurrence and the wood mouse Apodemus sylvaticus abundance the previous spring because they hosted tenfold more larvae than the bank vole Myodes glareolus. The bank vole abundance in spring and autumn had a negative and positive effect, respectively, on the nymph abundance. In agricultural landscapes, wood mice were positively influenced by woodland cover and woodland/hedgerow-grassland ecotone, whereas bank voles showed the opposite or non-significant responses to these landscape variables. The woodland cover had a positive effect on immature ticks. Conclusion: The landscape configuration, likely by affecting the landscape connectivity, influences the small mammal communities in permanent habitats. Our study showed that the wood mouse, due to its dominance and to its tolerance to ticks, feeds a substantial proportion of larvae. The acquired resistance to ticks in the bank vole can reduce its role as a trophic resource over time. The nymph abundance seems indirectly influenced by landscape features via their effects on the small mammal community. To enhance our understanding of the epidemiology of tick-borne diseases within landscapes, further studies will integrate data on pathogen prevalence and investigate explicitly the effect of landscape connectivity on host-vector-pathogen systems.
Published: 2016

50. Critical review on biofilm methods

Author: Joana Azeredo, Nuno F. Azevedo, Filipe Mergulhão, Miroslava Kačániová, Susanne Knøchel, Nuno Cerca, Anália Lourenço, Romain Briandet, Rikke Louise Meyer, Giovanni Di Bonaventura, Manuel Simões, Odile Tresse, Tom Coenye, Zoran Jaglic, Michel Hébraud, Ana Rita Costa, George Nychas, Claus Sternberg, Mickaël Desvaux, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Microbiologie Environnement Digestif Santé (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), SECurité des ALIments et Microbiologie, Institut National de la Recherche Agronomique (INRA)-École nationale d'ingénieurs des techniques des industries agricoles et alimentaires (ENITIAA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), Centre of Biological Engineering (CEB) - Laboratorios de Biofilmes Rosario Oliveira (LIBRO), University of Minho [Braga], LEPABE Department of Chemical Engineering - Faculty of Engineering, Universidade do Porto = University of Porto, Université Paris-Saclay, Laboratory of Pharmaceutical Microbiology, Universiteit Gent = Ghent University (UGENT), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Department of Medical, Oral, and Biotechnological Sciences, Università degli studi 'G. d'Annunzio' Chieti-Pescara [Chieti-Pescara] (Ud'A), Center of Excellence on Aging and Translational Medicine (CeSI-MeT), Department of Food and Feed Safety - Laboratory of Food Bacteriology, Veterinary Research Institute, Department of Microbiology - Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture, Department of Food Science [Copenhagen] (UCPH FOOD), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Department of Computer Science, Universidade de Vigo, Interdisciplinary Nanoscience Center (iNANO), Aarhus University [Aarhus], Laboratory of Microbiology and Biotechnology of Foods, Agricultural University of Athens, Institut National de la Recherche Agronomique (INRA)-École nationale d'ingénieurs des techniques des industries agricoles et alimentaires (ENITIAA)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), PRES Université Nantes Angers Le Mans (UNAM), Department of Biotechnology and Biomedicine, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Sécurité des Aliments (SECALIM), Ecole Nationale Vétérinaire de Nantes-Institut National de la Recherche Agronomique (INRA), Universidade do Minho, Faculdade de Engenharia, Universidade do Porto [Porto], Ghent University [Belgium] (UGENT), Microbiologie Environnement Digestif Santé - Clermont Auvergne (MEDIS), INRA Clermont-Ferrand-Theix-Université Clermont Auvergne (UCA), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Universidate de Vigo, UMR 1014 SECurité des ALIments et Microbiologie, Institut National de la Recherche Agronomique (INRA)-Département Microbiologie et Chaîne Alimentaire (MICA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-SECurité des ALIments et Microbiologie (SECALIM), Technical University of Denmark [Lyngby] (DTU), Universidade do Porto, Universiteit Gent = Ghent University [Belgium] (UGENT), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS), and Université Clermont Auvergne (UCA)-INRA Clermont-Ferrand-Theix
Subjects: Microbiological Techniques, 0301 basic medicine, BIOFILMS, Databases, Factual, [SDV]Life Sciences [q-bio], CATALYZED REPORTER DEPOSITION, Biofilm formation, biofilm data analysis, biofilm formation devices, biofilm measurement, biofilm omics, Applied Microbiology and Biotechnology, biofilm, Bacterial Adhesion, Biofilm omics, EXTRACELLULAR POLYMERIC SUBSTANCES, Lab-On-A-Chip Devices, Image Processing, Computer-Assisted, PSEUDOMONAS-AERUGINOSA BIOFILM, In Situ Hybridization, Fluorescence, ComputingMilieux_MISCELLANEOUS, Microscopy, SOLUBLE MICROBIAL PRODUCTS, Atomic force microscopy, IN-SITU, MICROSCOPY, Equipment Design, General Medicine, CANDIDA-ALBICANS BIOFILMS, omics, STAPHYLOCOCCUS-EPIDERMIDIS, HYBRIDIZATION, 030106 microbiology, LASER-SCANNING, Biology, Microbiology, 03 medical and health sciences, Extracellular polymeric substance, QUARTZ-CRYSTAL MICROBALANCE, Molecular Biology, ATOMIC-FORCE MICROSCOPY, Science & Technology, Critical perspective, Biofilm, Biology and Life Sciences, biochemical phenomena, metabolism, and nutrition, Biofilms, Biochemical engineering, Software
Abstract: Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms., The authors would like to acknowledge the support from the EU COST Action BacFoodNet FA1202.
Published: 2016

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