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14 results on '"Galleron, Nathalie"'

1. Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in advanced non-small cell lung cancer patients

Author

Derosa, Lisa, Routy, Bertrand, Thomas, Andrew Maltez, Iebba, Valerio, Zalcman, Gerard, Friard, Sylvie, Mazieres, Julien, Audigier-Valette, Clarisse, Moro-Sibilot, Denis, Goldwasser, François, Silva, Carolina Alves Costa, Terrisse, Safae, Bonvalet, Melodie, Scherpereel, Arnaud, Pegliasco, Hervé, Richard, Corentin, Ghiringhelli, François, Elkrief, Arielle, Desilets, Antoine, Blanc-Durand, Felix, Cumbo, Fabio, Blanco, Aitor, Boidot, Romain, Chevrier, Sandy, Daillère, Romain, Kroemer, Guido, Alla, Laurie, Pons, Nicolas, Chatelier, Emmanuelle Le, Galleron, Nathalie, Roume, Hugo, Dubuisson, Agathe, Bouchard, Nicole, Messaoudene, Meriem, Drubay, Damien, Deutsch, Eric, Barlesi, Fabrice, Planchard, David, Segata, Nicola, Martinez, Stéphanie, Zitvogel, Laurence, Soria, Jean-Charles, and Besse, Benjamin

Subjects
Lung Neoplasms, Carcinoma, Non-Small-Cell Lung, Humans, Immunologic Factors, Akkermansia, Immunotherapy, Article
Abstract

Aside from PD-L1 expression, biomarkers of response to immune checkpoint inhibitors (ICI) in non-small cell lung cancer (NSCLC) are needed. We previously reported in 100 NSCLC and kidney cancer patients that fecal Akkermansia muciniphila (Akk) correlated with ICI clinical success. The endpoint of this study was to prospectively validate the prognostic significance of fecal Akk in advanced NSCLC patients treated with first or second line ICI. We performed shotgun metagenomics-based microbiome profiling using two different pipelines in 338 NSCLC patients. Baseline stool Akk was associated with increased objective response rates and overall survival in multivariate analyses, independent of PD-L1 expression, antibiotics and performance status. Intestinal Akk was accompanied by a richer commensalism, including Eubacterium hallii and Bifidobacterium adolescentis and a more inflamed tumor microenvironment in a subset of patients. However, antibiotic use (20% of cases) coincided with a relative dominance of Akk above 4.8% accompanied with the genus Clostridium, both associated with resistance to ICI. Our study shows significant differences in relative abundance of Akk that could be useful for future studies as a tool to aid patient stratification.

Published
2022

2. Impairment of gut microbial biotin metabolism and host biotin status in severe obesity:effect of biotin and prebiotic supplementation on improved metabolism

Author

Belda, Eugeni, Voland, Lise, Tremaroli, Valentina, Falony, Gwen, Adriouch, Solia, Assmann, Karen E., Prifiti, Edi, Aron-Wisnewsky, Judith, Debedat, Jean, Le Roy, Tiphaine, Nielsen, Trine, Amouyal, Chloe, Andre, Sebastien, Andreelli, Fabrizio, Blueher, Matthias, Chakaroun, Rima, Chilloux, Julien, Coelho, Luis Pedro, Dao, Maria Carlota, Das, Promi, Fellahi, Soraya, Forslund, Sofia, Galleron, Nathalie, Hansen, Tue H., Holmes, Bridget, Ji, Boyang, Pedersen, Helle Krogh, Phuong Le, Le Chatelier, Emmanuelle, Lewinter, Christian, Manneras-Holm, Louise, Marquet, Florian, Myridakis, Antonis, Pelloux, Veronique, Pons, Nicolas, Quinquis, Benoit, Rouault, Christine, Roume, Hugo, Salem, Joe-Elie, Sokolovska, Nataliya, Søndertoft, Nadja B., Touch, Sothea, Vieira-Silva, Sara, Galan, Pilar, Holst, Jens, Gøtze, Jens Peter, Køber, Lars, Vestergaard, Henrik, Hansen, Torben, Hercberg, Serge, Oppert, Jean-Michel, Nielsen, Jens, Letunic, Ivica, Dumas, Marc-Emmanuel, Stumvoll, Michael, Pedersen, Oluf Borbye, Bork, Peer, Ehrlich, Stanislav Dusko, Zucker, Jean-Daniel, Baeckhed, Fredrik, Raes, Jeroen, Clement, Karine, Commission of the European Communities, Medical Research Council (MRC), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases [IHU ICAN], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Nutrition et obésités: approches systémiques (UMR-S 1269) (Nutriomics), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Inst Med, Dept Mol & Clin Med, Wallenberg Lab, University of Gothenburg (GU), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS (U1153 / UMR_A_1125 / UMR_S_1153)), Institut National de la Recherche Agronomique (INRA)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris Descartes - Paris 5 (UPD5)-Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Sorbonne Paris Cité (COMUE) (USPC), MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Université Pierre et Marie Curie - Paris 6 (UPMC)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Sorbonne Université (SU), Service de Nutrition [CHU Pitié-Salpétrière], Institut E3M [CHU Pitié-Salpêtrière], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Université de Bordeaux (UB), Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Service de Diabétologie [CHU Pitié-Salpétrière], Laboratoire de chimie Macromoléculaire (CNRS UMR 5076), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM), 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), Universität Leipzig [Leipzig], Keck School of Medicine [Los Angeles], University of Southern California (USC), Nutrition et cerveau (U1213, U855), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM), Instituto de Medicina Molecular, Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases - UMR 8199 - UMR 1283 (EGENODIA (GI3M)), Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Imperial College London - National Heart and Lung Institute, and Division of Computational and Systems Medicine, Imperial College London, London, SW7 2AZ, UK

Subjects
EXPRESSION, [SDV]Life Sciences [q-bio], Biotin, Endocrinology and Diabetes, Microbiology, DIET, Mice, Humans, Animals, Obesity, CHROMIUM PICOLINATE, Inflammation, Science & Technology, OVERWEIGHT, Gastroenterology & Hepatology, Gastroenterology, 1103 Clinical Sciences, Gastrointestinal Microbiome, Obesity, Morbid, MetaCardis Consortium, Mice, Inbred C57BL, nutrition, Prebiotics, Diabetes Mellitus, Type 2, Cardiovascular and Metabolic Diseases, micronutrients, Other Clinical Medicine, diabetes mellitus, Vitamin B Complex, 1114 Paediatrics and Reproductive Medicine, intestinal bacteria, HEALTH, Life Sciences & Biomedicine
Abstract

ObjectivesGut microbiota is a key component in obesity and type 2 diabetes, yet mechanisms and metabolites central to this interaction remain unclear. We examined the human gut microbiome’s functional composition in healthy metabolic state and the most severe states of obesity and type 2 diabetes within the MetaCardis cohort. We focused on the role of B vitamins and B7/B8 biotin for regulation of host metabolic state, as these vitamins influence both microbial function and host metabolism and inflammation.DesignWe performed metagenomic analyses in 1545 subjects from the MetaCardis cohorts and different murine experiments, including germ-free and antibiotic treated animals, faecal microbiota transfer, bariatric surgery and supplementation with biotin and prebiotics in mice.ResultsSevere obesity is associated with an absolute deficiency in bacterial biotin producers and transporters, whose abundances correlate with host metabolic and inflammatory phenotypes. We found suboptimal circulating biotin levels in severe obesity and altered expression of biotin-associated genes in human adipose tissue. In mice, the absence or depletion of gut microbiota by antibiotics confirmed the microbial contribution to host biotin levels. Bariatric surgery, which improves metabolism and inflammation, associates with increased bacterial biotin producers and improved host systemic biotin in humans and mice. Finally, supplementing high-fat diet-fed mice with fructo-oligosaccharides and biotin improves not only the microbiome diversity, but also the potential of bacterial production of biotin and B vitamins, while limiting weight gain and glycaemic deterioration.ConclusionStrategies combining biotin and prebiotic supplementation could help prevent the deterioration of metabolic states in severe obesity.Trial registration numberNCT02059538.

Published
2022
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3. Low FODMAP diet improves functional-like gastrointestinal symptoms but reduces bifidobacteria and faecalibacterium prausnitzii in Quiescent inflammatory bowel disease: a randomised controlled trial and metagenomic analysis

Author

Cox, S., Stagg, A., Fromentin, Sébastien, Ehrlich, Dusko, McCarthy, N., Galleron, Nathalie, Levenez, Florence, Lomer, M., Lindsay, J., Irving, P., Whelan, K., Nutritional Sciences, Texas Tech University [Lubbock] (TTU), Queen Mary University of London (QMUL), MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), King‘s College London, Nutrition and Dietetics, Harokopio University, Barts Health NHS Trust [London, UK], Guy's and St Thomas' NHS Foundation Trust, and European Crohn´s and Colitis Organisation (ECCO). INT.

Subjects
ComputingMilieux_MISCELLANEOUS, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology
Abstract

International audience

Published
2018
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4. Low fodmap diet improves functional-like gastrointestinal symptoms but reduces bifidobacteria in quiescent inflammatory bowel disease

Author

Cox, Selina, Stagg, Andrew, Fromentin, Sebastien, Ehrlich, Dusko, McCarthy, Neil, Galleron, Nathalie, Levenez, Florence, Lomer, Miranda, Lindsay, James, Irving, Peter, Whelan, Kevin, ProdInra, Migration, King‘s College London, Queen Mary University of London (QMUL), MetaGenoPolis, Institut National de la Recherche Agronomique (INRA), Guy's and St. Thomas' NHS Foundation Trust, Barts Hlth NHS Trust, and Partenaires INRAE

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2018

5. Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome

Author

Shoaie, Saeed, Ghaffari, Pouyan, Kovatcheva-Datchary, Petia, Mardinoglu, Adil, Sen, Partho, Pujos-Guillot, Estelle, De Wouters, Tomas, Juste, Catherine, Rizkalla, Salwa, Chilloux, Julien, Hoyles, Lesley, Nicholson, Jeremy K., Consortium, MICRO-Obes, Doré, Joël, Dumas, Marc E., Clément, Karine, Bäckhed, Fredrik, Nielsen, Jens, Kennedy, Sean P., Prifti, Edi, Pons, Nicolas, Le Chatelier, Emmanuelle, Almeida, Mathieu, Quinquis, Benoit, Levenez, Florence, Galleron, Nathalie, Batto, Jean-Michel, Ehrlich, Stanislav, Blottiere, Herve, Lepage, Patricia, Maguin, Emmanuelle, Van De Guchte, Maarten, Department of Biology and Biological Engineering, Chalmers University of Technology [Göteborg], University of Gothenburg (GU), Unité de Nutrition Humaine (UNH), Institut National de la Recherche Agronomique (INRA)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université, Plateforme d'Exploration du Métabolisme, 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, MetaGenoPolis, CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Institute of cardiometabolism and nutrition (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Imperial College London, University of Copenhagen = Københavns Universitet (KU), Département Microbiologie et Chaîne Alimentaire (MICA), Knut and Alice Wallenberg Foundation, Bill & Melinda Gates Foundation, Torsten Soderbergs Stiftelse, European Commission HEALTH-F4-2012-305312, Fondation Coeur et Arteres, French National Agency of Research (ANR MicroObes and 'Investissements d'avenir') ANR-10-IAHU-05, ProdInra, Migration, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases (ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Institut de Cardiométabolisme et Nutrition = Institute of Cardiometabolism and Nutrition [CHU Pitié Salpêtrière] (IHU ICAN), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU)-CHU Pitié-Salpêtrière [AP-HP], University of Copenhagen = Københavns Universitet (UCPH), Plateforme Exploration du Métabolisme (PFEM), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-MetaboHUB-Clermont, MetaboHUB-MetaboHUB, Commission of the European Communities, and Université d'Auvergne - Clermont-Ferrand I (UdA)-Clermont Université-Institut National de la Recherche Agronomique (INRA)

Subjects
Male, HOST, Interactive optimization, Physiology, Genome scale, Microbial metabolism, Computational biology, Gut flora, Bioinformatics, Models, Biological, MICROFLORA, Endocrinology & Metabolism, RECONSTRUCTIONS, 03 medical and health sciences, 0302 clinical medicine, Human gut, MICRO-Obes Consortium, 1101 Medical Biochemistry And Metabolomics, Humans, Metabolic modeling, AMINO-ACIDS, Microbiome, Intestinal Mucosa, Molecular Biology, Feces, 030304 developmental biology, 0303 health sciences, Science & Technology, biology, Microbiota, 0601 Biochemistry And Cell Biology, Cell Biology, biology.organism_classification, GENE, Intestines, PROTEIN-COUPLED RECEPTOR, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, CHAIN FATTY-ACIDS, HUMAN LARGE-INTESTINE, BACTERIA, Female, ADIPOSITY, Life Sciences & Biomedicine, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, 030217 neurology & neurosurgery
Abstract

International audience; The human gut microbiome is known to be associated with various human disorders, but a major challenge is to go beyond association studies and elucidate causalities. Mathematical modeling of the human gut microbiome at a genome scale is a useful tool to decipher microbe-microbe, diet-microbe and microbe-host interactions. Here, we describe the CASINO (Community And Systems-level INteractive Optimization) toolbox, a comprehensive computational platform for analysis of microbial communities through metabolic modeling. We first validated the toolbox by simulating and testing the performance of single bacteria and whole communities in vitro. Focusing on metabolic interactions between the diet, gut microbiota, and host metabolism, we demonstrated the predictive power of the toolbox in a diet-intervention study of 45 obese and overweight individuals and validated our predictions by fecal and blood metabolomics data. Thus, modeling could quantitatively describe altered fecal and serum amino acid levels in response to diet intervention.

Published
2015
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6. Characterization of the gut microbiota by quantitative metagenomics: a promising tool for risk stratification in NAFLD patients

Author

Ratziu, V., Pichaud, M., Fedchuk, L., Levenez, Florence, Quinquis, Benoit, Galleron, Nathalie, Batto, Jean-Michel, Pons, Nicolas, Le Chatelier, Emmanuelle, Almeida, Mathieu, Kennedy, Sean, Doré, Joël, Ehrlich, Stanislav, Rimbaud, P., CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Enterome Bioscience, Association Recherche Maladies Hépatiques Virales, Partenaires INRAE, MetaGenoPolis, and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], nafld, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2013

7. Dietary intervention impact on gut microbial gene richness

Author

Cotillard, Aurélie, Kennedy, Sean P., Kong, Ling Chun, Prifti, Edi, Pons, Nicolas, Le Chatelier, Emmanuelle, Almeida, Mathieu, Quinquis, Benoit, Levenez, Florence, Galleron, Nathalie, Gougis, Sophie, Rizkalla, Salwa, Batto, Jean-Michel, Renault, Pierre, consortium, ANR MicroObes, Doré, Joel, Zucker, Jean-Daniel, Clément, Karine, Ehrlich, Stanislav Dusko, Blottière, Hervé, Leclerc, Marion, Juste, Catherine, de Wouters, Tomas, Lepage, Patricia, Fouqueray, Charlene, Basdevant, Arnaud, Henegar, Cornelieu, Godard, Cindy, Fondacci, Marine, Rohia, Alili, Hajduch, Froogh, Weissenbach, Jean, Pelletier, Eric, Le Paslier, Denis, Gauchi, Jean-Pierre, Gibrat, Jean-François, Loux, Valentin, Carré, Wilfrid, Maguin, Emmanuelle, van de Guchte, Maarten, Jamet, Alexandre, Boumezbeur, Fouad, Layec, Séverine, U872 Centre de Recherche des Cordeliers, Nutriomique, Équipe 7, Centre de Recherche des Cordeliers (CRC (UMR_S 872)), Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), MetaGénoPolis, Institut National de la Recherche Agronomique (INRA), Centre de Recherche en Nutrition Humaine d'Ile-de-France (CRNH Ile-de-France), Institute of Cardiometabolism and Nutrition, Assistance Publique - Hôpitaux de Paris, MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] (UMMISCO), Université Cadi Ayyad [Marrakech] (UCA)-Universtié Yaoundé 1 [Cameroun]-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), MetaGenoPolis, Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université de Yaoundé I-Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cadi Ayyad [Marrakech] (UCA), Université Cadi Ayyad [Marrakech] (UCA)-Université de Yaoundé I-Université Gaston Bergé (Saint-Louis, Sénégal)-Université Cheikh Anta Diop [Dakar, Sénégal] (UCAD)-Institut de la francophonie pour l'informatique-Université Pierre et Marie Curie - Paris 6 (UPMC), Centre de Recherche des Cordeliers ( CRC (UMR_S 872) ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Institut National de Recherche Agronomique, MICrobiologie de l'ALImentation au Service de la Santé humaine ( MICALIS ), Institut National de la Recherche Agronomique ( INRA ) -AgroParisTech, Unité de modélisation mathématique et informatique des systèmes complexes [Bondy] ( UMMISCO ), and Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut de la francophonie pour l'informatique-Université Cheikh Anta Diop ( UCAD ) -Université Gaston Bergé (Saint-Louis, Sénégal)-Universtié Yaoundé 1 [Cameroun]-University Cadi Ayyad ( UCA )

Subjects
index, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, obesity, Zoology, 030209 endocrinology & metabolism, Overweight, Gut flora, resistance, 03 medical and health sciences, 0302 clinical medicine, Weight loss, medicine, insulin sensitivity, overweight, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Multidisciplinary, biology, business.industry, biology.organism_classification, medicine.disease, Obesity, 3. Good health, Biotechnology, Metagenomics, inflammation, Genomic Profile, mass, Enterotype, Species richness, medicine.symptom, business
Abstract

Complex gene-environment interactions are considered important in the development of obesity(1). The composition of the gut microbiota can determine the efficacy of energy harvest from food(2-4) and changes in dietary composition have been associated with changes in the composition of gut microbial populations(5,6). The capacity to explore microbiota composition was markedly improved by the development of metagenomic approaches(7,8), which have already allowed production of the first human gut microbial gene catalogue(9) and stratifying individuals by their gut genomic profile into different enterotypes(10), but the analyses were carried out mainly in nonintervention settings. To investigate the temporal relationships between food intake, gut microbiota and metabolic and inflammatory phenotypes, we conducted diet-induced weight-loss and weight-stabilization interventions in a study sample of 38 obese and 11 overweight individuals. Here we report that individuals with reduced microbial gene richness (40%) present more pronounced dys-metabolism and low-grade inflammation, as observed concomitantly in the accompanying paper(11). Dietary intervention improves low gene richness and clinical phenotypes, but seems to be less efficient for inflammation variables in individuals with lower gene richness. Low gene richness may therefore have predictive potential for the efficacy of intervention.

Published
2013
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8. Extending the cereus group genomics to putative food-borne pathogens of different toxicity

Author

Lapidus, Alla, Goltsman, Eugene, Auger, Sandrine, Galleron, Nathalie, Segurens, Beatrice, Dossat, Carole, Land, Miriam L., Broussole, Veronique, Brillard, Julien, Guinebretiere, Marie-Helene, Sanchis, Vincent, Nguen-the, Christophe, Lereclus, Didier, Richardson, Paul, Winker, Patrick, Weissenbach, Jean, Ehrlich, S.Dusko, and Sorokin, Alexei

Subjects
cereus genomics, Life Sciences
Abstract

The cereus group represents sporulating soil bacteria containing pathogenic strains which may cause diarrheic or emetic food poisoning outbreaks. Multiple locus sequence typing revealed a presence in natural samples of these bacteria of about thirty clonal complexes. Application of genomic methods to this group was however biased due to the major interest for representatives closely related to B. anthracis. Albeit the most important food-borne pathogens were not yet defined, existing data indicate that they are scattered all over the phylogenetic tree. The preliminary analysis of the sequences of three genomes discussed in this paper narrows down the gaps in our knowledge of the cereus group. The strain NVH391-98 is a rare but particularly severe food-borne pathogen. Sequencing revealed that the strain must be a representative of a novel bacterial species, for which the name Bacillus cytotoxis is proposed. This strain has a reduced genome size compared to other cereus group strains. Genome analysis revealed absence of sigma B factor and the presence of genes encoding diarrheic Nhe toxin, not detected earlier. The strain B. cereus F837/76 represents a clonal complex close to that of B. anthracis. Including F837/76, three such B. cereus strains had been sequenced. Alignment of genomes suggests that B. anthracis is their common ancestor. Since such strains often emerge from clinical cases, they merit a special attention. The third strain, KBAB4, is a typical psychrotrophe characteristic to unbiased soil communities. Phylogenic studies show that in nature it is the most active group in terms of gene exchange. Genomic sequence revealed high presence of extra-chromosomal genetic material (about 530 kb) that may account for this phenomenon. Genes coding Nhe-like toxin were found on a big plasmid in this strain. This may indicate a potential mechanism of toxicity spread from the psychrotrophic strain community. The results of this genomic work and ecological compartments of different strains incite to consider a necessity of creating prophylactic vaccines against bacteria closely related to NVH391-98 and F837/76. Presumably developing of such vaccines can be based on the properties of non-pathogenic strains such as KBAB4 or ATCC14579 reported here or earlier. By comparing the protein coding genes of strains being sequenced in this project to others we estimate the shared proteome in the cereus group to be 3,000?b200 genes and the total proteome to be 20-25,000 genes.

Published
2008

9. The complete genome sequence of the gram-positive bacterium Bacillus subtilis

Author

Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, Vasco, Bertero, M.G., Bessières, Philippe, Bolotin, A., Borchert, S., Borriss, R., Boursier, L., Brans, A., Braun, Marie, Brignell, S.C., Bron, S., Brouillet, S., Capuano, V., Ehrlich, S.D., Galleron, Nathalie, Lapidus, A., Pujic, Petar, Serror, Pascale, Sorokin, A., Zumstein, Emmanuelle, Unité de recherche Génétique Microbienne (UGM), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV.BC]Life Sciences [q-bio]/Cellular Biology
Abstract

49 ref. 5 graph.; International audience

Published
1997

10. The complete genome sequence of the gram-positive bacterium Bacillus subtilis

Author

Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, Vasco, Bertero, M.G., Bessières, Philippe, Bolotin, A., Borchert, S., Borriss, R., Boursier, L., Brans, A., Braun, Marie, Brignell, S.C., Bron, S., Brouillet, S., Capuano, V., Ehrlich, S.D., Galleron, Nathalie, Lapidus, A., Pujic, Petar, Serror, Pascale, Sorokin, A., Zumstein, Emmanuelle, and ProdInra, Migration

Subjects
[SDV.BC] Life Sciences [q-bio]/Cellular Biology
Published
1997

11. Specificity of insertion of Tn 1545 transposon family in Lactococcus lactis subsp. lactis

Author

Renault, P., Nogrette, J.F., Galleron, Nathalie, Godon, Jean-Jacques, Ehrlich, S.D., Unité de recherche Génétique Microbienne (UGM), Institut National de la Recherche Agronomique (INRA), Institut francilien recherche, innovation et société (IFRIS), Institut National de la Recherche Agronomique (INRA)-École des hautes études en sciences sociales (EHESS)-OST-Université Paris-Est Marne-la-Vallée (UPEM)-Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.)-ESIEE Paris-Centre National de la Recherche Scientifique (CNRS), J.J. Ferretti, M.S. Gilmore, T.R. Klahenhammer, F. Brown, and Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.)-Institut National de la Recherche Agronomique (INRA)-École des hautes études en sciences sociales (EHESS)-OST-Université Paris-Est Marne-la-Vallée (UPEM)-ESIEE Paris-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
1995

12. Specificity of insertion of Tn1545 transposon family in Lactococcus lactis subsp. lactis

Author

Renault, P., Nogrette, J.F., Galleron, Nathalie, Godon, Jean-Jacques, Unité de recherche Génétique Microbienne (UGM), Institut National de la Recherche Agronomique (INRA), J.J. Ferretti, and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], LACTOCOCCUS LACTIS
Abstract

*INRA, centre de Jouy Diffusion du document : INRA, centre de Jouy

Published
1994

13. Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species

Author

Rey, Michael W, Ramaiya, Preethi, Nelson, Beth A, Brody-Karpin, Shari D, Zaretsky, Elizabeth J, Tang, Maria, de Leon, Alfredo Lopez, Xiang, Henry, Gusti, Veronica, Clausen, Ib Groth, Olsen, Peter B, Rasmussen, Michael D, Andersen, Jens T, Jørgensen, Per L, Larsen, Thomas S, Sorokin, Alexei, Bolotin, Alexander, Lapidus, Alla, Galleron, Nathalie, Ehrlich, S Dusko, and Berka, Randy M

Subjects
Spores, Bacterial, Protein Transport, Research, Prophages, Molecular Sequence Data, DNA Transposable Elements, bacteria, Siderophores, Bacillus, Genomics, Genome, Bacterial, Anti-Bacterial Agents, Bacillus subtilis
Abstract

The complete sequence of the Bacillus licheniformis ATCC 14580 genome was determined, revealing 4,208 predicted protein-coding genes, 7 rRNA operons and 72 tRNA genes., Background Bacillus licheniformis is a Gram-positive, spore-forming soil bacterium that is used in the biotechnology industry to manufacture enzymes, antibiotics, biochemicals and consumer products. This species is closely related to the well studied model organism Bacillus subtilis, and produces an assortment of extracellular enzymes that may contribute to nutrient cycling in nature. Results We determined the complete nucleotide sequence of the B. licheniformis ATCC 14580 genome which comprises a circular chromosome of 4,222,336 base-pairs (bp) containing 4,208 predicted protein-coding genes with an average size of 873 bp, seven rRNA operons, and 72 tRNA genes. The B. licheniformis chromosome contains large regions that are colinear with the genomes of B. subtilis and Bacillus halodurans, and approximately 80% of the predicted B. licheniformis coding sequences have B. subtilis orthologs. Conclusions Despite the unmistakable organizational similarities between the B. licheniformis and B. subtilis genomes, there are notable differences in the numbers and locations of prophages, transposable elements and a number of extracellular enzymes and secondary metabolic pathway operons that distinguish these species. Differences include a region of more than 80 kilobases (kb) that comprises a cluster of polyketide synthase genes and a second operon of 38 kb encoding plipastatin synthase enzymes that are absent in the B. licheniformis genome. The availability of a completed genome sequence for B. licheniformis should facilitate the design and construction of improved industrial strains and allow for comparative genomics and evolutionary studies within this group of Bacillaceae.

Published
2004

14. Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer

Author

Lisa Derosa, Bertrand Routy, Andrew Maltez Thomas, Valerio Iebba, Gerard Zalcman, Sylvie Friard, Julien Mazieres, Clarisse Audigier-Valette, Denis Moro-Sibilot, François Goldwasser, Carolina Alves Costa Silva, Safae Terrisse, Melodie Bonvalet, Arnaud Scherpereel, Hervé Pegliasco, Corentin Richard, François Ghiringhelli, Arielle Elkrief, Antoine Desilets, Felix Blanc-Durand, Fabio Cumbo, Aitor Blanco, Romain Boidot, Sandy Chevrier, Romain Daillère, Guido Kroemer, Laurie Alla, Nicolas Pons, Emmanuelle Le Chatelier, Nathalie Galleron, Hugo Roume, Agathe Dubuisson, Nicole Bouchard, Meriem Messaoudene, Damien Drubay, Eric Deutsch, Fabrice Barlesi, David Planchard, Nicola Segata, Stéphanie Martinez, Laurence Zitvogel, Jean-Charles Soria, Benjamin Besse, Derosa, Lisa, Routy, Bertrand, Thomas, Andrew Maltez, Iebba, Valerio, Zalcman, Gerard, Friard, Sylvie, Mazieres, Julien, Audigier-Valette, Clarisse, Moro-Sibilot, Deni, Goldwasser, Françoi, Silva, Carolina Alves Costa, Terrisse, Safae, Bonvalet, Melodie, Scherpereel, Arnaud, Pegliasco, Hervé, Richard, Corentin, Ghiringhelli, Françoi, Elkrief, Arielle, Desilets, Antoine, Blanc-Durand, Felix, Cumbo, Fabio, Blanco, Aitor, Boidot, Romain, Chevrier, Sandy, Daillère, Romain, Kroemer, Guido, Alla, Laurie, Pons, Nicola, Le Chatelier, Emmanuelle, Galleron, Nathalie, Roume, Hugo, Dubuisson, Agathe, Bouchard, Nicole, Messaoudene, Meriem, Drubay, Damien, Deutsch, Eric, Barlesi, Fabrice, Planchard, David, Segata, Nicola, Martinez, Stéphanie, Zitvogel, Laurence, Soria, Jean-Charle, and Besse, Benjamin

Subjects
metagenomics, Lung Neoplasms, Microbiota, Programmed Cell Death 1 Receptor, biomarkers, kidney cancer, General Medicine, Akkermansia, patients stratification, NSCLC, General Biochemistry, Genetics and Molecular Biology, B7-H1 Antigen, Microbiome, immunotherapy, Akkermansia muciniphila, cancer, immune checkpoint inhibitors (ICIs), tumor microenvironment, Carcinoma, Non-Small-Cell Lung, Tumor Microenvironment, biomarker, Humans, metagenomic, Retrospective Studies
Abstract

Aside from PD-L1 expression, biomarkers of response to immune checkpoint inhibitors (ICIs) in non-small-cell lung cancer (NSCLC) are needed. In a previous retrospective analysis, we documented that fecal Akkermansia muciniphila (Akk) was associated with clinical benefit of ICI in patients with NSCLC or kidney cancer. In the current study, we performed shotgun-metagenomics-based microbiome profiling in a large cohort of patients with advanced NSCLC (n = 338) treated with first- or second-line ICIs to prospectively validate the predictive value of fecal Akk. Baseline stool Akk was associated with increased objective response rates and overall survival in multivariate analyses, independent of PD-L1 expression, antibiotics, and performance status. Intestinal Akk was accompanied by a richer commensalism, including Eubacterium hallii and Bifidobacterium adolescentis, and a more inflamed tumor microenvironment in a subset of patients. However, antibiotic use (20% of cases) coincided with a relative dominance of Akk above 4.8% accompanied with the genus Clostridium, both associated with resistance to ICI. Our study shows significant differences in relative abundance of Akk that may represent potential biomarkers to refine patient stratification in future studies.

Published
2020

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