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133 results on '"Institut de Recherche pour le Développement ( IRD ) -Aix Marseille Université ( AMU )"'

1. Neobacillus massiliamazoniensis sp. nov., a new bacterial species isolated from stool sample of an inhabitant of the Amazon region

Author

Mbaye, B., Tidjani Alou, M., Fadlane, A., Fregiere, L., Alibar, S., Million, M., Fenollar, F., Lo, C.I., Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Neobacillus massiliamazoniensis, Culturomics, gut microbiota, taxonogenomics, Infectious and parasitic diseases, RC109-216, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, genome, ComputingMilieux_MISCELLANEOUS, Taxonogenomics: Genome of a New Organism
Abstract

Using a culturomics approach, a strain was isolated, identified and characterised following the taxonogenomics concept. Neobacillus massiliamazoniensis sp. nov., strain LF1T (=CSURP1359) was isolated from human stool. The 16S rRNA gene sequence analysis of strain LF1T (accession number: LK021124) exhibits 98.32% similarity levels with Neobacillus bataviensis strain IDA1115 (accession number: NR_036766.1), the phylogenetically closest related species with standing in nomenclature. The draft genome size of strain LF1T (accession number: CVRB00000000) is 4.6 Mbp with a G+C content of 34.1 mol%. Analysis of phylogenic tree, genomic analysis and phenotypic criteria described here sufficiently prove that this bacterium is different from previously known bacterial species with standing in nomenclature and represents a new Neobacillus species belonging to Firmicutes phylum.

Published
2021

2. Draft genome of Metabacillus niabensis strain 4T19T isolated from cotton-waste composts for mushroom cultivation

Author

Luis Johnson Kangale, Eric Ghigo, P.-E. Fournier, Didier Raoult, Anthony Levasseur, Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, 030106 microbiology, Infectious and parasitic diseases, RC109-216, Biology, Microbiology, Genome, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Metabacillus niabensis strain 4T19T, Botany, mushroom, DSMZ, German Collection of Microorganisms and Cell Cultures, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Cotton-waste, genome, ComputingMilieux_MISCELLANEOUS, Whole genome sequencing, Mushroom, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Contig, Strain (chemistry), CSUR, Collection de Souches de l’Unitédes Rickettsies, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Infectious Diseases, planarian, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Taxonogenomics: Genome of a Known Organism
Abstract

In this article, we present the draft genome sequence of Metabacillus niabensis strain 4T19T (= CSUR Q2603 T = DSM 17723 = JCM 16399 = KACC 11279), that is a new Metabacillus species isolated from cotton-waste composts. The genome sequence from Metabacillus niabensis strain 4T19T was assembled into 462 contigs for a total size of 4,987,608 bp with a G + C content of 35.5%.

Published
2021

3. Investigations by the Institut Hospitalo-Universitaire Méditerranée Infection of food and food-borne infections in the Mediterranean Basin and in sub-Saharan Africa

Author

Jean-Marc Rolain, Philippe Colson, C. Abat, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
Paper, 0301 basic medicine, medicine.medical_specialty, Sub saharan, 030106 microbiology, Developing country, food-borne, virus, Microbiology, Mediterranean Basin, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Environmental health, medicine, lcsh:RC109-216, infections, bacteria, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Transmission (medicine), food, Public health, fungus, digestive, oral, and skin physiology, Zoonosis, zoonosis, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, IHU Mediterranée Infection, 030104 developmental biology, Infectious Diseases, Geography, Food products, Food borne, Africa
Abstract

Food-borne infections are major causes of public health concern in developing and developed countries. During the past decade, the Institut Hospitalo-Universitaire Méditerranée Infection has conducted or been involved in multiple investigations that aimed at identifying the sources and strains responsible for food-borne diseases and therefore at improving the understanding, diagnosis, prevention and control of these infections. Investigations were conducted in the Mediterranean area and in sub-Saharan Africa on more than 15 food-borne agents, 17 food products and 14 antibiotic resistance-associated genes. Multiple sources, including unexpected ones, and pathogens, including emerging ones, were involved. Travelling in developing countries and zoonoses are major contributors to food-borne infections, while food-borne transmission of resistance-associated genes is increasingly reported. However, risk factors and pathogens associated with food-borne infections likely remain untapped and must be more extensively investigated, monitored and regularly reassessed. Diagnostic tests based on new technologies and real-time surveillance tools based on microbiology laboratory data are promising approaches to detect known food-borne infections and decipher new ones. Studies of the microbiota and its relationships with dietary patterns are also worth being conducted. Keywords: Africa, bacteria, food, food-borne, fungus, IHU Mediterranée Infection, infections, Mediterranean Basin, virus, zoonosis

Published
2018

4. Correlative light electron microscopy of giant viruses with the SECOM system

Author

Julien Andreani, S. Hari, D. Sahmi-Bounsiar, Jean-Pierre Baudoin, S.I. Traore, B. La Scola, Jacques Bou-Khalil, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Assistance Publique - Hôpitaux de Marseille (APHM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
0301 basic medicine, Correlative, Materials science, Scanning electron microscope, Microbiology, law.invention, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Nuclear magnetic resonance, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, law, Microscopy, Giant Virus, lcsh:RC109-216, Amoeba, giant viruses, ComputingMilieux_MISCELLANEOUS, Ultramicrotomy, Tupanvirus, CLEM, SECOM system, 030104 developmental biology, Infectious Diseases, Transmission electron microscopy, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Ultrastructure, Original Article, Electron microscope
Abstract

Bright-field transmission electron microscopy (TEM), TEM-negative staining technique, resin-embedding and ultramicrotomy, scanning TEM, scanning electron microscopy, atomic force microscopy and cryoelectron microscopy are imaging techniques used for describing giant viruses, their cycle and ultrastructure. Here we used the SECOM system, an integrated correlative light and electron microscopy using light and electronic imaging without sample transfer, to study cells infected with giant viruses, as shown by Tupanvirus, the ultrastructure of which was successfully observed. An improvement of the SECOM system with an eye to its use in fundamental and clinical research could be considered in the field of microbiology. Keywords: Amoeba, CLEM, giant viruses, SECOM system, Tupanvirus

Published
2018

5. MALDI-TOF MS and point of care are disruptive diagnostic tools in Africa

Author

Eric Chabrière, Cheikh Sokhna, Hubert Bassene, Michel Drancourt, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
Paper, MALDI-TOF, 0301 basic medicine, medicine.medical_specialty, 030106 microbiology, 030231 tropical medicine, Mass spectrometry, Diagnostic tools, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, borne vectors, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Medical physics, bacteria, Arthropods, ComputingMilieux_MISCELLANEOUS, Point of care, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, business.industry, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, point of care, 3. Good health, Matrix-assisted laser desorption/ionization, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, business
Abstract

We review reviewing our experience of point-of-care and mass spectrometry in Senegal as two disruptive technologies promoting the rapid diagnosis of infection, permitting better medical management of patients. Keywords: Arthropods, bacteria, borne vectors, MALDI-TOF, point of care

Published
2018

6. Naming microorganisms: the contribution of the IHU Méditerranée Infection, Marseille, France

Author

Didier Raoult, Melhem Bilen, Michel Drancourt, Frédéric Cadoret, B. La Scola, P.-E. Fournier, J.-C. Lagier, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010)

Subjects
Paper, 0301 basic medicine, New bacterial species, Microbiological culture, Microorganism, Zoology, Giant virus, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Common species, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Nomenclature, ComputingMilieux_MISCELLANEOUS, Culturomics, Taxonogenomics, Human microbiome, Isolation (microbiology), Archaea, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, 030104 developmental biology, Infectious Diseases, Geography, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Human microbiota, Sample collection
Abstract

The number of isolated new microorganisms has dramatically increased after the readaption of culture using the culturomics approach. Each of these microorganisms is deposited in an international strain collection institute, with its name being attributed and published by the scientist who isolated it. The attributed name is of Latin or Latinized origin and chosen on the basis of the geographical location of the sample collection, the institute or geographical region where the project was being performed, the name of a concerned scientist, and characteristics of the sample or the microorganism. Our institution has played an important role in the isolation of new microorganisms, with the first effort reporting 468 new bacterial species (3% of the bacterial species isolated at least once worldwide) and 327 species isolated for the first time from human beings, which in turn resulted in an increase of 30% of the total number of microorganisms isolated. Additionally, more than 100 giant viruses, including seven new species, have been isolated at our institute. In the present work, after recalling the rules of nomenclature, we detail the naming of the new microorganisms chosen at our laboratory. The most common species name was massiliensis, attributed 161 times. We consider it imperative for the cultivators, who have frequently made considerable efforts in the field of microbial culture, to be the ones who name the newly isolated microorganisms, taking into consideration the Latinized nomenclature standards. Keywords: Archaea, Culturomics, Giant virus, Human microbiota, New bacterial species, Taxonogenomics

Published
2018

7. Virgibacillus doumboii sp. nov., a halophilic bacterium isolated from the stool of a healthy child in Mali

Author

Nicholas Armstrong, M. Million, Mahamadou Ali Thera, Abdoulaye Djimde, M. Tidjani Alou, Safiatou Niare, Aminata Camara, Didier Raoult, Salimata Konate, Cheikh Ibrahima Lo, Florence Fenollar, A. Hamidou Togo, Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Université des sciences, des techniques et des technologies de Bamako (USTTB), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, 030106 microbiology, Infectious and parasitic diseases, RC109-216, taxonogenomics, Mali, Microbiology, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Virgibacillus, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Genome size, Gene, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, Phylogenetic tree, Virgibacillus doumboii sp. nov, Child malnutrition, Ribosomal RNA, culturomics, biology.organism_classification, 16S ribosomal RNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, 030104 developmental biology, Infectious Diseases, Culturomics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Bacteria, Taxonogenomics: Genome of a New Organism
Abstract

A moderately halophilic and strictly aerobic bacterium was isolated from a human stool as part of a study on the diagnosis of childhood malnutrition in Mali. Strain Marseille-Q1616T is a Gram-stain-positive, rod-shaped, catalase-positive and oxidase-negative bacterium. It has a genome size of 3.91 Mbp with 39.79% G+C content, which contains 3954 protein-coding genes including genes encoding phosphomycin resistance and Listeria monocytogenes, 16 rRNA genes and 64 tRNA genes. Strain Marseille-Q1616T exhibited a 96.3% 16S rRNA gene sequence similarity and shared an OrthoANI value of 70.64% (the highest observed) with Virgibacillus kekensis, the phylogenetically closest validly published species. Based on phenotypic and phylogenetic evidence and genomic average nucleotide identity values, we suggest the creation of a new species within the Virgibacillus genus, named Virgibacillus doumboii sp. nov., type strain Marseille-Q1616T (= CSURQ1616).

Published
2021

8. Genome analysis of Lachnoclostridium phocaeense isolated from a patient after kidney transplantation in Marseille

Author

I. Dandachi, H. Anani, L. Hadjadj, S. Brahimi, J.-C. Lagier, Z. Daoud, J.-M. Rolain, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Balamand [Liban] (UOB), ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), and University of Balamand - UOB (LIBAN)

Subjects
Lachnoclostridium new species taxonogenomics, new species, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Bacteria, Infectious and parasitic diseases, RC109-216, taxonogenomics, culturomics, Lachnoclostridium, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Bacteria culturomics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Taxonogenomics: Genome of a New Organism
Abstract

International audience; Lachnoclostridium phocaeense is a new species in the genus Lachnoclostridium. Lachnoclostridium phocaeense is a Gram-positive anaerobic rod. This strain, Marseille-P3177T (CSUR = P3177) with the below described genome was isolated from the urine sample of a women after kidney transplantation. The strain genome is 3 500 754 bp long with 50.62% G + C content and consists of a single contig (GenBank accession number NZ_LT635479.1).

Published
2021

9. What could explain the late emergence of COVID-19 in Africa?

Author

Jean-Marc Rolain, Didier Raoult, Cheikh Sokhna, Sofiane Bakour, Christian Devaux, Rym Lalaoui, Bruno Pradines, Pierre Verger, Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Observatoire régional de la santé Provence-Alpes-Côte d'Azur [Marseille] (ORS PACA), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030106 microbiology, antimalarial drugs, malaria, medicine.disease_cause, acute respiratory syndrome coronavirus 2, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, coronavirus disease 2019, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Pandemic, medicine, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, China, ComputingMilieux_MISCELLANEOUS, Coronavirus, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Respiratory tract infections, SARS-CoV-2, Social distance, severe, COVID-19, Mini-Review, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Malaria, 030104 developmental biology, Infectious Diseases, Geography, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Africa, Antimalarial drugs, Demography, severe acute respiratory syndrome coronavirus 2
Abstract

At the end of November 2019, a novel coronavirus responsible for respiratory tract infections emerged in China. Despite drastic containment measures, this virus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), spread in Asia and Europe. The pandemic is ongoing with a particular hotspot in southern Europe and America in spring 2020. Many studies predicted an epidemic in Africa similar to that currently seen in Europe and the USA. However, reported data do not confirm these predictions. Several hypotheses that could explain the later emergence and spread of the coronavirus disease 2019 (COVID-19) pandemic in African countries are being discussed, including the lack of health-care infrastructure capable of clinically detecting and confirming COVID-19 cases, the implementation of social distancing and hygiene, international air traffic flows, the climate, the relatively young and rural population, the genetic polymorphism of the angiotensin-converting enzyme 2 receptor, cross-immunity and the use of antimalarial drugs.

Published
2020

10. Genome sequence and description of Urinicoccus timonensis gen. nov., sp. nov., a new bacterium isolated from a human stool sample

Author

Didier Raoult, Florence Fenollar, Anthony Fontanini, Jeremy Delerce, Cheikh Ibrahima Lo, Anthony Levasseur, Mamadou Lamine Tall, E. Kuete Yimagou, Pierre-Edouard Fournier, CCSD, Accord Elsevier, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, Stool sample, [SDV]Life Sciences [q-bio], 030106 microbiology, Peptoniphilaceae, New Species, Microbiology, Genome, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, lcsh:RC109-216, Gut, Bacterial genomics, Urinicoccus timonensisgen. nov., sp. nov, Whole genome sequencing, Genetics, Culturomics, biology, Taxonogenomics, Strain (biology), 16S ribosomal RNA, biology.organism_classification, 6. Clean water, [SDV] Life Sciences [q-bio], 030104 developmental biology, Infectious Diseases, Bacteria
Abstract

International audience; Urinicoccus timonensis gen. nov., sp. nov. strain Marseille-P3926(T) is a new species from the phylum Firmicutes and the family Peptoniphilaceae that was isolated from a human faeces sample. Genome was 1 978 908 bp long with a 41.1 G + C content. The closest species based on 16S ribosomal RNA was Peptoniphilus ivorii DSM 10022 with 90.8% sequence similarity. Considering phenotypic features, 16S rRNA sequence and comparative genome studies, we proposed Marseille-P3926(T) as the strain type of Urinicoccus timonensis gen. nov., sp. nov. (C) 2020 The Authors. Published by Elsevier Ltd.

Published
2020

11. Peripherally inserted central catheters: a hidden emerging cause of infection outbreaks

Author

Didier Raoult, Nadim Cassir, Cédric Abat, Guillaume André Durand, V. Vidal, Marie-Thérèse Jimeno, P. Brouqui, Florence Fenollar, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, medicine.medical_specialty, hospital-acquired infection, business.industry, [SDV]Life Sciences [q-bio], 030106 microbiology, Outbreak, bloodstream infection, medicine.disease, Microbiology, mortality, lcsh:Infectious and parasitic diseases, 3. Good health, 03 medical and health sciences, 030104 developmental biology, Infectious Diseases, Bloodstream infection, Hospital-acquired infection, Emergency medicine, medicine, Bacteraemia, lcsh:RC109-216, Original Article, PICC Line, business
Abstract

In our institution, between January 2010 and December 2017, 15 140 peripherally inserted central catheters (PICCs) were inserted in 12 314 patients. Using time-series analysis to evaluate the annual historical trend (AHT), we observed a significant increase in bloodstream infections (BSIs; AHT = 24; p < 0.001) and associated deaths (AHT = 3; p 0.02) in patient with PICCs. The risk of experiencing a BSI was significantly higher in patients with PICCs (odds ratio = 9.6; 95% confidence interval, 9.08-10.18; p < 0.001). To reduce PICC-related BSIs and their related mortality, it is important to limit the overuse of PICCs and to implement a `no PICC' policy by limiting the insertion of PICCs to situations without other available options. (C) 2020 The Author(s). Published by Elsevier Ltd.

Published
2020

12. Parabacteroides pacaensis sp. nov. and Parabacteroides provencensis sp. nov., two new species identified from human gut microbiota

Author

Gérard Aboudharam, S.I. Traore, A. Fadlane, S. Benabdelkader, Sabrina Naud, B. La Scola, Cheikh Ibrahima Lo, Chimie Et Interdisciplinarité : Synthèse, Analyse, Modélisation (CEISAM), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
0301 basic medicine, 030106 microbiology, medicine.disease_cause, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Human gut, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, human gut microbiota, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, Parabacteroides provencensis sp. nov, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, lcsh:RC109-216, ComputingMilieux_MISCELLANEOUS, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Culturomics, Strain (chemistry), biology, Parabacteroides chinchillae, New Specie, 16S ribosomal RNA, Parabacteroides, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Parabacteroides pacaensis sp. nov, 030104 developmental biology, Infectious Diseases, Parabacteroides gordonii, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, new bacteria, Bacteria
Abstract

Strains Marseille-P4001 and Marseille-P3668 are new species from the order Bacteroidales isolated from healthy French volunteers. They are anaerobic Gram-negative rod-shaped bacteria. They exhibited 92.68% and 96.68% 16S rRNA sequence identities with Parabacteroides gordonii strain MS-1 and Parabacteroides chinchillae JCM 17104, respectively, the phylogenetically closest species. Their respective draft genomes measured 5.23 Mb and 3.73 Mb with 39.2 mol% and 40.8 mol% of G + C content. Using a taxonogenomics method, we propose here a brief description of Parabacteroides pacaensis sp. nov., strain Marseille-P4001T and Parabacteroides provencensis sp. nov., strain Marseille-P3668T as new bacterial species. Keywords: Culturomics, human gut microbiota, new bacteria, Parabacteroides pacaensis sp. nov., Parabacteroides provencensis sp. nov

Published
2020

13. Dialister massiliensis sp. nov., a new bacterium isolated from the human gut

Author

Didier Raoult, Grégory Dubourg, Pamela Afouda, Pierre-Edouard Fournier, Enora Tomei, Aix Marseille Université (AMU), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, Firmicutes, 030106 microbiology, Genus Dialister, taxonogenomics, Gut flora, Microbiology, digestive system, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Human gut, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Dialister massiliensis sp. nov, ComputingMilieux_MISCELLANEOUS, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Culturomics, biology, gut microbiota, Family Veillonellaceae, New Specie, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, 030104 developmental biology, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Dialister, Bacteria
Abstract

Dialister massiliensis strain Marseille-P5638T (= CSUR P5638) is a new species from the genus Dialister and family Veillonellaceae which was isolated from the gut microbiota of a healthy individual. Keywords: Culturomics, Dialister massiliensis sp. nov., Firmicutes, gut microbiota, taxonogenomics

Published
2020

14. Noncontiguous finished genome sequence and description of Bartonella mastomydis sp. nov

Author

Florence Fenollar, Hubert Bassene, Noémie Labas, L. Granjon, Didier Raoult, Oleg Mediannikov, Mustapha Dahmani, Awa Diop, Georges Diatta, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
ESPECE NOUVELLE, 0301 basic medicine, Bartonella, TRANSMISSION, complete genome, BACTERIE, Biology, Microbiology, Genome, Bartonella mastomydis sp. nov, lcsh:Infectious and parasitic diseases, RONGEUR, GENETIQUE DE POPULATION, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Mastomys erythroleucus, lcsh:RC109-216, Gene, ComputingMilieux_MISCELLANEOUS, Whole genome sequencing, Genetics, Strain (biology), RNA, Ribosomal RNA, bacterial infections and mycoses, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Senegal, GENOME, 030104 developmental biology, Infectious Diseases, rodents, Original Article, RESERVOIR, GC-content
Abstract

Bartonella mastomydis sp. nov. strain 008 is the type strain of B. mastomydis sp. nov., a new species within the genus Bartonella. This strain was isolated from Mastomys erythroleucus rodents trapped in the Sine-Saloum region of Senegal. Here we describe the features of this organism, together with the complete genome sequence and its annotation. The 2 044 960 bp long genomes with 38.44% G + C content contains 1674 protein-coding and 42 RNA genes, including three rRNA genes. Keywords: Bartonella mastomydis sp. nov., complete genome, Mastomys erythroleucus, rodents, Senegal

Published
2018

15. Olsenella timonensis sp. nov., a new bacteria species isolated from the human gut microbiota

Author

Ndongo, S., Tall, M.L., Ngom, I.I., Delerce, J., Levasseur, A., Raoult, D., Fournier, P.-E., Khelaifia, S., Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Culturomics, Taxonogenomics, Gut microbiota, Olsenella timonensis sp. nov, New Specie, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, digestive system, lcsh:Infectious and parasitic diseases, Anaerobic culture, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, lcsh:RC109-216, ComputingMilieux_MISCELLANEOUS
Abstract

Olsenella timonensis sp. nov., strain Marseille-P2300T (= CSUR P2300; =DSM102072), is a new bacterial species from the phylum Firmicutes in the family Atopobiaceae.This bacteria species was isolated from the human gut microbiota. Keywords: Anaerobic culture, Culturomics, Gut microbiota, Olsenella timonensis sp. nov., Taxonogenomics

Published
2019

16. Prevotella ihumii sp. nov., a new bacterium isolated from a stool specimen of a healthy woman

Author

Didier Raoult, Hussein Anani, Anthony Fontanini, E. Guilhot, Claudia Andrieu, Pierre-Edouard Fournier, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
0301 basic medicine, taxono-genomics, 030106 microbiology, Prevotella ihumii, Stool specimen, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, fluids and secretions, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, stomatognathic system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, otorhinolaryngologic diseases, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, lcsh:RC109-216, ComputingMilieux_MISCELLANEOUS, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Culturomics, Strain (chemistry), biology, New Specie, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, stomatognathic diseases, 030104 developmental biology, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, human activities, Bacteria
Abstract

Prevotella ihumii strain Marseille-P3385T (= CSURP3385T; = DSM106428T) is a new species isolated from a fresh stool specimen of a healthy woman. Keywords: Culturomics, Prevotella ihumii, taxono-genomics

Published
2019

17. Malaria, tuberculosis and HIV: what's new? Contribution of the Institut Hospitalo-Universitaire Méditerranée Infection in updated data

Author

Michel Drancourt, Lionel Almeras, Philippe Parola, Bruno Pradines, Christian Devaux, Leonardo K. Basco, Cheikh Sokhna, Stéphane Ranque, Philippe Brouqui, Département d’Infectiologie de Terrain, Unité de Parasitologie, Institut de Recherche Biomédicale des Armées (IRBA), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Biomédicale des Armées [Antenne Marseille] (IRBA), Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, Paper, medicine.medical_specialty, Tuberculosis, 030231 tropical medicine, 030106 microbiology, Plasmodium falciparum, Human immunodeficiency virus (HIV), malaria, medicine.disease_cause, Microbiology, drugs, lcsh:Infectious and parasitic diseases, Mycobacterium tuberculosis, resistance, 03 medical and health sciences, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, parasitic diseases, medicine, microbiota, lcsh:RC109-216, Vector (molecular biology), Diagnostic, Intensive care medicine, ComputingMilieux_MISCELLANEOUS, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, business.industry, Diagnostic test, HIV, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Infectious Diseases, tuberculosis, business, vector, Malaria
Abstract

The Institut Hospitalo-Universitaire Méditerranée Infection is positioned for the diagnosis, prevention and treatment of the ‘big three’ killer diseases: malaria, tuberculosis and HIV. We implemented the use of new diagnostic samples such as stools and new diagnostic tests such as mass spectrometry for the dual identification of vectors and pathogens. Furthermore, advances in the prevention and treatment of malaria and tuberculosis are reviewed, along with advances in the understanding of the role of microbiota in the resistance to HIV infection. These achievements represent a major step towards a better management of the ‘big three’ diseases worldwide. Keywords: Diagnostic, drugs, HIV, malaria, microbiota, Mycobacterium tuberculosis, Plasmodium falciparum, resistance, tuberculosis, vector

Published
2018

18. ‘Cellulomonas timonensis’ sp. nov., taxonogenomics description of a new bacterial species isolated from human gut

Author

Pierre-Edouard Fournier, F. Di Pinto, J.-C. Lagier, Catherine Robert, S. Ndongo, Mamadou Beye, Fadi Bittar, Didier Raoult, Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
0301 basic medicine, taxonogenomics, Biology, Microbiology, Genome, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Genus, human gut microbiota, lcsh:RC109-216, Cellulomonas, Gene, genome, ComputingMilieux_MISCELLANEOUS, Whole genome sequencing, Strain (chemistry), culturomics, biology.organism_classification, Phenotype, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 6. Clean water, 030104 developmental biology, Infectious Diseases, Culturomics, Cellulomonas timonensis, Original Article
Abstract

‘Cellulomonas timonensis’ sp. nov. strain sn7T is a new species within the Cellulomonas genus. We present the main phenotypic characteristics and provide a complete annotation of its genome sequence. This facultative anaerobic bacterium, isolated from the stool of 38-year-old obese Frenchman, is Gram-positive, has motile rods and is sporulating. The genome is 4 057 828 bp long with 72.42% G + C content. Of the 3732 predicted genes, 3667 were protein-coding genes and 65 were RNAs. Keywords: Cellulomonas timonensis, culturomics, genome, human gut microbiota, taxonogenomics

Published
2018

19. Noncontiguous finished genome sequence and description of Mediterranea massiliensis gen. nov., sp. nov., a new member of the Bacteroidaceae family isolated from human colon

Author

Didier Raoult, A. Benezech, Nicholas Armstrong, Issa Isaac Ngom, Frédéric Cadoret, M. Mailhe, Anthony Levasseur, Saber Khelaifia, D. Ricaboni, Caroline Michelle, Véronique Vitton, M. Million, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Hôpital Nord [CHU - APHM], Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), INSB-INSB-Centre National de la Recherche Scientifique (CNRS), and HAL AMU, Administrateur

Subjects
0301 basic medicine, Colon, taxonogenomics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, Genome, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Genus, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, sp. nov, lcsh:RC109-216, genome, Bacteroidaceae, Nomenclature, Genetics, Whole genome sequencing, biology, Strain (chemistry), culturomics, biology.organism_classification, Mediterranea massiliensis gen. nov, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Infectious Diseases, Culturomics, GenBank, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

Strain Marseille-P2645T was isolated in a colon sample from a Frenchwoman who underwent a colonoscopy. Bacterial cells were Gram negative, non–spore forming, mobile and strictly anaerobic. The genome of strain Marseille-P2645T is 3 950 441 bp long and contains 3374 protein-coding genes. The DNA G+C content is of 51.66 mol%. Strain Marseille-P2645T exhibited a 92.9% sequence similarity with Bacteroides helcogenes strain P36-108T (GenBank accession no. CP002352), the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2645T (= CSUR P2645 = DSM 103034) is therefore a candidate as a type species of a new genus belonging to the Bacteroidaceae family, for which the name of Mediterranea massiliensis gen. nov., sp. nov., is proposed. Keywords: Colon, culturomics, genome, Mediterranea massiliensis gen. nov., sp. nov., taxonogenomics

Published
2018

20. NMNI editorial report, 2020

Author

Michel Drancourt, P.-E. Fournier, Ghiles Grine, Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
History, Editorial activities, Library science, Infectious and parasitic diseases, RC109-216, Microbiology, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, editorial manuscript, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, editorial report, ComputingMilieux_MISCELLANEOUS, report, 030304 developmental biology, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, New Microbes and New Infections, 030306 microbiology, Visibility (geometry), Window (computing), [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Clinical microbiology, Editorial, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Abstract

Since its launch 7 years ago, in 2013, New Microbes and New Infections (NMNI) has published a total of 773 of the 1300 submitted papers retrievable in PubMed Central (Fig. 1). NMNI aims to provide access to an international forum for authors reporting facts in infectious and primarily tropical diseases and clinical microbiology that are new in one place and country. Accordingly, NMNI acknowledges contributions from emerging research teams, offering authors the opportunity to publish in their own language, in addition to English; in 2020, two manuscripts have been submitted in non-English languages (French). In the meantime, NMNI has been included in PubMed Central, obviously increasing its visibility and the interest of authors and readers. Open in a separate window Fig. 1 Submitted manuscripts and editorial outcomes 2016–2020 (Elsevier data).

Published
2021

21. Dakarella massiliensis gen. nov., sp. nov., strain ND3T: a new bacterial genus isolated from the female genital tract

Author

Didier Raoult, Niokhor Dione, Pierre-Edouard Fournier, Florence Bretelle, Florence Fenollar, J. Rathored, Catherine Robert, J.-C. Lagier, Enora Tomei, Saber Khelaifia, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Unité des Rickettsies et pathogènes émergents (URPE), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48

Subjects
0301 basic medicine, Genetics, Strain (chemistry), taxono-genomics, culturomics, Biology, 16S ribosomal RNA, biology.organism_classification, Microbiology, Genome, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Infectious Diseases, Culturomics, Genus, lcsh:RC109-216, Original Article, Sutterella wadsworthensis, Gene, Nomenclature, bacterial vaginosis
Abstract

International audience; Strain ND3(T) was isolated from the genital tract of a 28-year-old woman with bacterial vaginosis. This strain exhibited a 16S rRNA gene sequence similarity of 92.4% with Sutterella wadsworthensis, the phylogenetically closest species with standing in nomenclature. Strain ND3(T) was a strictly anaerobic Gram-negative rod and member of the family Sutterellaceae. It exhibited a genome of 2 476 884 bp containing 2175 protein-coding and 62 RNA genes. On the basis of these data, we propose the creation of 'Dakarella massiliensis' sp. nov. with strain ND3(T) (= CSUR P1938 = DSM 100447) as the type strain.

Published
2017

22. Description of ‘Arabia massiliensis’ gen. nov., sp. nov., ‘Gordonibacter massiliensis’ sp. nov., and ‘Bacilliculturomica massiliensis’ gen. nov., sp. nov., isolated from a faecal specimen of a 50-year-old Saudi Bedouin woman

Author

E.I. Azhar, Jeremy Delerce, Asif Ahmad Jiman-Fatani, Didier Raoult, Pierre-Edouard Fournier, Fehmida Bibi, Frédéric Cadoret, Muhammad Yasir, J.-C. Lagier, S.I. Traore, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), King Abdulaziz University, King Fahd Medical Research Center, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48

Subjects
0106 biological sciences, 0301 basic medicine, Gordonibacter, ‘Arabia massiliensis’, gut microbiota, New Species, ‘Bacilliculturomica massiliensis’, Biology, 010603 evolutionary biology, 01 natural sciences, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, 'Bacilliculturomica massiliensis', 030104 developmental biology, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Culturomics, 'Gordonibacter massiliensis', 'Arabia massiliensis', ‘Gordonibacter massiliensis’, lcsh:RC109-216
Abstract

International audience; We report here the main characteristics of 'Arabia massiliensis' strain Marseille-P3078(T) gen. nov., sp. nov., 'Gordonibacter massiliensis' Marseille-P2775(T) sp. nov. and 'Bacilliculturomica massiliensis' strain Marseille-P3303 gen. nov., sp. nov. The culturomics approach combined with taxonogenomics was used to characterize these strains, which were all isolated from a faecal specimen of a 50-year-old Saudi Bedouin woman.

Published
2017

23. Massilioclostridium coli gen. nov., sp. nov., a new member of the Clostridiaceae family isolated from the left colon of a 27-year-old woman

Author

Lo, C., Mailhe, M., Ricaboni, D., Vitton, V., Benezech, A., Michelle, C., Armstrong, N., Bittar, F., Fournier, Pierre-Edouard, Raoult, Didier, Lagier, J.-C., Direction des Ressources Marines et Minières, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Assistance Publique - Hôpitaux de Marseille (APHM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Massilioclostridium coli, Colon, microbiota, lcsh:RC109-216, taxonogenomics, culturomics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, lcsh:Infectious and parasitic diseases, Taxonogenomics: Genome of a New Organism
Abstract

International audience; Massilioclostridium coli gen. nov., sp. nov., a new member of the Clostridiaceae family isolated from the left colon of a 27-year-old woman Abstract Massilioclostridium coli strain Marseille-P2976 T (= CSUR P2976 = DSM 103344) is a new bacterial genus isolated from the left colon of a patient who underwent colonoscopy for colorectal cancer screening. Massilioclostridium coli is a Gram-negative bacillus, strict anaerobic, nonsporogenous and nonmotile organism. We describe here the strain Marseille-P2976 T and provide its complete annotated genome sequence according to taxonogenomics concepts. Its genome is 2 985 330 bp long and contains 2562 predicted genes and 75 RNA genes.

Published
2017
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24. Taxonogenomics and description of Vaginella massiliensis gen. nov., sp. nov., strain Marseille P2517 T , a new bacterial genus isolated from the human vagina

Author

Caroline Michelle, Didier Raoult, P.-E. Fournier, Florence Fenollar, Magali Richez, Florence Bretelle, Khoudia Diop, J. Rathored, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Unité des Rickettsies et pathogènes émergents (URPE), INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48

Subjects
0301 basic medicine, biology, Obligate, Vaginal flora, Strain (biology), vaginal flora, Bacterial vaginosis, biology.organism_classification, 16S ribosomal RNA, Vaginella massiliensis, Microbiology, Flavobacteriaceae, Genome, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Infectious Diseases, Type (biology), Genus, New Microbes in Humans, lcsh:RC109-216, genome
Abstract

International audience; An obligate aerobic, Gram-negative, nonmotile and nonsporulating rod designated Marseille P2517 was isolated from the vaginal flora. We describe its features, annotate the genome and compare it to the closest species. The 16S rRNA analysis shows 93.03% sequence similarity with Weeksella virosa, the phylogenetically closest species. Its genome is 2 434 475 bp long and presents 38.16% G+C. On the basis of these data, it can be considered as a new genus in the Flavobacteriaceae family, for which we proposed the name Vaginella massiliensis gen. nov., sp. nov. The type strain is Marseille P2517(T).

Published
2017
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25. Bartonella massiliensis sp. nov., a new bacterial species isolated from an Ornithodoros sonrai tick from Senegal

Author

Hussein Anani, Hacène Medkour, Oleg Mediannikov, Florence Fenollar, Cheikh Ibrahima Lo, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), and Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
0301 basic medicine, Bartonella, Bartonella massiliensissp. nov, 030106 microbiology, Ornithodoros sonrai, Tick, Microbiology, lcsh:Infectious and parasitic diseases, soft tick, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, stomatognathic system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, hemic and lymphatic diseases, senegal, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, cardiovascular diseases, genome, ComputingMilieux_MISCELLANEOUS, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, biology.organism_classification, bacterial infections and mycoses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Infectious Diseases, Recurrent fever, Vector (epidemiology), [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Taxonogenomics: Genome of a Known Organism, bacteria, Genus Bartonella
Abstract

Bartonella massiliensis sp. nov., strain OS09T (= CSURB624T = DSM 23169), is the type strain of Bartonella massiliensis sp. nov., a new species within the genus Bartonella. It was isolated from a soft tick, Ornithodoros sonrai, vector of recurrent fever collected from Senegalese domestic rodent burrows. This strain is an aerobic, rod-shaped and Gram-negative bacterium. On the basis of taxonogenomic approach, we propose the creation of Bartonella massiliensis sp. nov. Keywords: Bartonella massiliensissp. nov., genome, Ornithodoros sonrai, senegal, soft tick

Published
2019

26. Leprosy in French Polynesia

Author

V. Vialette, C. Rovery, N.L. Nguyen, Didier Musso, Ahmed Loukil, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
0301 basic medicine, medicine.medical_specialty, Pediatrics, Medical staff, 030106 microbiology, Population, Prevalence, French Polynesia, Microbiology, World health, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, National level, lcsh:RC109-216, education, ComputingMilieux_MISCELLANEOUS, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, education.field_of_study, business.industry, Public health, Article(s) from the Special Issue on Infections in Polynesia, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Pacific, 3. Good health, 030104 developmental biology, Infectious Diseases, Infectious disease (medical specialty), [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Leprosy, business, leprosy
Abstract

Leprosy is a neglected endemic infectious disease in the Pacific region. In French Polynesia (FP), leprosy is no longer a public health problem at the national level, defined by the World Health Organization as a prevalence rate below 1 case per 10,000 population. However, even if its incidence has dramatically declined in FP in the last decades, leprosy is still endemic at a low level. Here we present a case of leprosy in a 34-year-old man from FP diagnosed in 2018. Clinical and microbiologic examinations, including fluorescence in-situ hybridization, led to the diagnosis of a multibacillary leprosy, and multidrug therapy was initiated. There is a need to maintain leprosy surveillance and trained medical staff for the detection and treatment of new cases. Keywords: French Polynesia, leprosy, Pacific

Published
2019

27. Anaerotruncusmassiliensis sp. nov., a succinate-producing bacterium isolated from human stool from an obese patient after bariatric surgery

Author

Pierre-Edouard Fournier, M. Million, Awa Diop, Magali Richez, Grégory Dubourg, Nicholas Armstrong, Saber Khelaifia, Amadou Hamidou Togo, Didier Raoult, Marie Maraninchi, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
0301 basic medicine, medicine.medical_specialty, obesity, food.ingredient, caractère phénotypique, 030106 microbiology, Médecine humaine et pathologie, microbiome, taxonogenomics, Biology, medicine.disease_cause, microbial culturomics, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, food, Anaerotruncus, human gut microbiome, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Anaerotruncus colihominis, Gene, bactérie, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, base nucléotidique, Strain (chemistry), Nucleic acid sequence, culturomics, 16S ribosomal RNA, biology.organism_classification, succinate, chirurgie bariatrique, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Surgery, obésité, 030104 developmental biology, Infectious Diseases, Culturomics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Human health and pathology, Original Article, Bacteria
Abstract

A new bacterium, strain AT3T, was isolated by microbial culturomics from a faecal sample from a Frenchman after bariatric surgery. The isolate exhibited 96.6% 16S ribosomal RNA gene nucleotide sequence similarity with Anaerotruncus colihominis strain WAL 14565T = CCUG 45055T = CIP 107754T. Phenotypic and genomic characteristics showed that the new strain represents a novel species, for which the name Anaerotruncus massiliensis sp. nov. is proposed. The type strain is strain AT3T = CSUR P2007T = DSM 100567T. Keywords: Anaerotruncus, human gut microbiome, microbial culturomics, obesity, taxonogenomics

Published
2019

28. Mobile populations across the Mediterranean Sea and beyond: travel medicine, mass gathering medicine and homeless health

Author

Bruno Pradines, Ziad A. Memish, Philippe Gautret, P. Parola, Cheikh Sokhna, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, Paper, homeless, medicine.medical_specialty, 030106 microbiology, education, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Mediterranean sea, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Mass gathering, Hajj, medicine, Travel medicine, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, lcsh:RC109-216, Socioeconomics, ComputingMilieux_MISCELLANEOUS, travel, Mass gathering medicine, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, mass gathering, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, Infectious Diseases, Geography, networks, Tropical medicine, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, surveillance, Grand Magal
Abstract

The Méditerranée Infection institute is internationally recognized for its expertise in infectious diseases and tropical medicine, and is one of the most active research centres for infectious diseases in Europe. Surveillance and research addressing infectious diseases in globally mobile populations is one of the strong components of the research conducted at the institute. A significant amount of clinical, microbiologic and epidemiologic works have been conducted in international travellers, pilgrims participating in large international religious gatherings, economic migrants and homeless migrant people over the last decades by our group. Our strong anchoring in several countries around the Mediterranean Sea and beyond, as well as the pivotal role of Marseille in the EuroTravNet and GeoSentinel international networks that monitor travel-associated diseases, reinforce our leading position in the fields of travel and tropical medicine, mass gathering medicine and homeless health. Keywords: Grand Magal, Hajj, homeless, mass gathering, networks, surveillance, travel

Published
2018

29. ‘Lactobacillus raoultii’ sp. nov., a new bacterium isolated from the vaginal flora of a woman with bacterial vaginosis

Author

Melhem Bilen, Frédéric Cadoret, Florence Bretelle, Florence Fenollar, B. Nicaise, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Balamand [Liban] (UOB), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), INSB-INSB-Centre National de la Recherche Scientifique (CNRS), University of Balamand - UOB (LIBAN), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), and Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
0301 basic medicine, 030106 microbiology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Lactobacillus, medicine, lcsh:RC109-216, human microbiota, vaginal microbiota, biology, Vaginal flora, Human microbiome, New Specie, Bacterial vaginosis, culturomics, biology.organism_classification, Isolation (microbiology), medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, 030104 developmental biology, Infectious Diseases, Culturomics, emerging bacteria, Lactobacillus raoultii, Bacteria
Abstract

We report the isolation of a new bacterium species, ‘Lactobacillus raoultii’ strain Marseille P4006 (CSUR P4006), isolated from a vaginal sample of a 45-year-old woman with bacterial vaginosis. Keywords: Bacterial vaginosis, culturomics, emerging bacteria, human microbiota, Lactobacillus raoultii, vaginal microbiota

Published
2017

30. Description of ‘Blautia phocaeensis’ sp. nov. and ‘Lachnoclostridium edouardi’ sp. nov., isolated from healthy fresh stools of Saudi Arabia Bedouins by culturomics

Author

Didier Raoult, E.I. Azhar, Pierre-Edouard Fournier, Frédéric Cadoret, Sory Ibrahima Traore, Jeremy Delerce, Fehmida Bibi, Asif Ahmad Jiman-Fatani, J.-C. Lagier, Muhammad Yasir, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), King Abdulaziz University, King Fahd Medical Research Center, Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48

Subjects
0301 basic medicine, new species, gut microbiota, taxono-genomics, Strain (biology), 030106 microbiology, 'Lachnoclostridium edouardi', Biology, Microbiology, 3. Good health, lcsh:Infectious and parasitic diseases, ‘Blautia phocaeensis’, 03 medical and health sciences, 030104 developmental biology, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Culturomics, ‘Lachnoclostridium edouardi’, lcsh:RC109-216, Lachnoclostridium, 'Blautia phocaeensis'
Abstract

International audience; We report here the main characteristics of 'Blautia phocaeensis' strain Marseille-P3441 sp. nov. and 'Lachnoclostridium edouardi' strain Marseille-P3397 sp. nov., that were isolated from a faecal specimen of a 42-year-old female Saudi Bedouin. We used a bacterial culturomics approach combined with taxono-genomics.

Published
2017

31. 'Negativibacillus massiliensis' gen. nov., sp. nov., isolated from human left colon

Author

M. Mailhe, Didier Raoult, D. Ricaboni, Claudia Andrieu, Pierre-Edouard Fournier, Véronique Vitton, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Service De Gastroenterologie, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48

Subjects
0301 basic medicine, Culturomics, Strain (chemistry), New Species, education, 030106 microbiology, taxonogenomics, "Negativibacillus massiliensis", Biology, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Infectious Diseases, Left colon, Human gut, Intestinibacillus massiliensis, microbiota, “Negativibacillus massiliensis”, lcsh:RC109-216, human gut
Abstract

International audience; We report here the main characteristics of "Negativibacillus massiliensis" strain Marseille-P3213(T), isolated from a human left-colon wash sample.

Published
2017

32. ‘Angelakisella massiliensis’ gen. nov., sp. nov., a new bacterial species isolated from human ileum

Author

Mailhe, M., Ricaboni, D., Vitton, V., Cadoret, F., Fournier, P.-E., Raoult, D., Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Service De Gastroenterologie, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
taxonomy, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, gut microbiota, Angelakisella massiliensis, New Species, genomics, lcsh:RC109-216, culturomics, lcsh:Infectious and parasitic diseases
Abstract

International audience; We present here a summary of the main characteristics of 'Angelakisella massiliensis' strain Marseille-P3217(T) (= CSUR P3217) that was isolated from the ileum liquid sample of a 76-year-old woman.

Published
2017

33. ‘Arcanobacterium urinimassiliense’ sp. nov., a new bacterium isolated from the urogenital tract

Author

Didier Raoult, Aurélie Morand, Khoudia Diop, Pierre-Edouard Fournier, J.C. Dubus, Florence Fenollar, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Unité des Rickettsies et pathogènes émergents (URPE), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), and INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48

Subjects
0301 basic medicine, 030106 microbiology, education, New Species, Biology, Rotavirus gastroenteritis, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, taxonomy, lcsh:RC109-216, human microbiota, health care economics and organizations, Genitourinary system, culturomics, biology.organism_classification, Virology, 3. Good health, rotavirus gastroenteritis, 030104 developmental biology, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Culturomics, ‘Arcanobacterium urinimassiliense’, Urine sample, Bacteria, Arcanobacterium urinimassiliense, 'Arcanobacterium urinimassiliense'
Abstract

Herein we report the main characteristics of 'Arcanobacterium urinimassiliense' strain Marseille-P3248T (=CSUR P3248) isolated from a urine sample of a 54-day-old girl with rotavirus gastroenteritis.

Published
2017

34. ‘Acidaminococcus timonensis’ sp. nov. and ‘Acidaminococcus massiliensis’ sp. nov. isolated from human gut

Author

A. Benezech, Didier Raoult, Frédéric Cadoret, M. Mailhe, Pierre-Edouard Fournier, D. Ricaboni, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Assistance Publique - Hôpitaux de Marseille (APHM), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48

Subjects
0301 basic medicine, Strain (chemistry), ‘Acidaminococcus massiliensis’, New Species, 030106 microbiology, culturomics, Biology, Acidaminococcus massiliensis, 16. Peace & justice, ‘Acidaminococcus timonensis’, Microbiology, lcsh:Infectious and parasitic diseases, 3. Good health, 03 medical and health sciences, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Infectious Diseases, Human gut, 'Acidaminococcus massiliensis', Culturomics, Acidaminococcus timonensis, microbiota, lcsh:RC109-216, 'Acidaminococcus timonensis', human gut
Abstract

International audience; We report here the main characteristics of 'Acidaminococcus timonensis' strain Marseille-P2764(T), isolated from human right colon, and 'Acidaminococcus massiliensis' strain Marseille-P2828(T), isolated from human duodenum.

Published
2017

35. ‘Lachnoclostridium urinimassiliense’ sp. nov. and ‘Lachnoclostridium phocaeense’ sp. nov., two new bacterial species isolated from human urine after kidney transplantation

Author

Didier Raoult, Frédéric Cadoret, S. Brahimi, Valérie Moal, Pierre-Edouard Fournier, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Unité de Recherche sur les Maladies Infectieuses Tropicales Emergentes (URMITE), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), and INSB-INSB-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48

Subjects
0301 basic medicine, Lachnoclostridium urinimassiliense, Culturomics, 030106 microbiology, New Species, kidney transplantation, Urine, Biology, medicine.disease, Microbiology, Lachnoclostridium phocaeense, lcsh:Infectious and parasitic diseases, 3. Good health, 03 medical and health sciences, taxonomy, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Infectious Diseases, medicine, lcsh:RC109-216, Kidney transplantation
Abstract

International audience; We describe here the main features of 'Lachnoclostridium urinimassiliense' strain Marseille-P2804(T) (= CSUR P2804) and 'Lachnoclostridium phocaeense' strain Marseille-P3177(T) (= CSUR P3177) that were isolated from urine samples after kidney transplantation in two women.

Published
2017

36. Description of Clostridium cagae sp. nov., Clostridium rectalis sp. nov. and Hathewaya massiliensis sp. nov., new anaerobic bacteria isolated from human stool samples

Author

Mamadou Lamine Tall, Didier Raoult, Pierre-Edouard Fournier, T.-P.-T. Pham, E. Kuete Yimagou, Cheikh Ibrahima Lo, Anthony Levasseur, S. Ndongo, Florence Fenollar, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
0301 basic medicine, Hathewaya massiliensis sp. nov, [SDV]Life Sciences [q-bio], 030106 microbiology, malnutrition, taxonogenomics, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Clostridium, lcsh:RC109-216, Clostridiaceae, Nomenclature, Clostridium cagae sp. nov, human immunodeficiency virus, biology, Strain (chemistry), culturomics, biology.organism_classification, Phylogenetic reconstruction, 030104 developmental biology, Infectious Diseases, Culturomics, Clostridium rectalis sp. nov, Anaerobic bacteria, Bacteria
Abstract

International audience; Using culturomics methods, three strains were isolated, identified and characterized following the taxonogenomics concept. Clostridium cagae strain Marseille-P4344(T) (=CSURP4344), Clostridium rectalis strain Marseille-P4200(T) (=CSURP4200) and Hathewaya massiliensis strain Marseille-P3545(T) (=CSURP3545) were isolated from human stool samples. The phylogenetic reconstruction, phenotypic criteria and genomic analyses were carried out and demonstrated that these three bacteria are different from previously known bacterial species with standing in nomenclature and were classified as new members of the Clostridiaceae family. (C) 2020 The Authors. Published by Elsevier Ltd.

Published
2020

37. Nullane salus extra ecclesiam

Author

Philippe Gautret, Didier Raoult, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
0301 basic medicine, medicine.medical_specialty, 2019-20 coronavirus outbreak, [SDV]Life Sciences [q-bio], Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030106 microbiology, Group comparison, Microbiology, Article, lcsh:Infectious and parasitic diseases, law.invention, 03 medical and health sciences, Clinical trials, Randomized controlled trial, law, medicine, lcsh:RC109-216, Intensive care medicine, SARS-CoV-2, business.industry, Public health, Chloroquine derivatives, COVID-19, Outbreak, In silico comparison, 3. Good health, Clinical trial, 030104 developmental biology, Infectious Diseases, Infectious disease (medical specialty), business
Abstract

Randomized clinical trials are not relevant for infectious disease outbreaks due to a new pathogen, for which public health decisions have to be made urgently. An approach based on group comparisons, in silico, may provide valuable results in a reasonably short period of time for a negligible amount of money. (C) 2020 The Authors. Published by Elsevier Ltd.

Published
2020

38. Megasphaera vaginalis sp. nov. and Anaerococcus vaginimassiliensis sp. nov., new bacteria isolated from vagina of French woman with bacterial vaginosis

Author

Khoudia Diop, Edmond Kuete Yimagou, B. Nicaise, Didier Raoult, Florence Fenollar, Cheikh Ibrahima Lo, Alexia Bordigoni, Christelle Desnues, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
0301 basic medicine, Firmicutes, 030106 microbiology, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Megasphaera, medicine, lcsh:RC109-216, Culturomics, Bacteria, Taxonogenomics, biology, Phylogenetic tree, Phylum, Anaerococcus, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Infectious Diseases, Anaerococcus vaginimassiliensis sp. nov, Vagina, Bacterial vaginosis, Megasphaera vaginalis sp. nov, Taxonogenomics: Genome of a New Organism
Abstract

International audience; Using the culturomics method, two strains were isolated, identified and characterized following the taxonogenomics concept. Megasphaera vaginalis sp. nov. strain Marseille-P4512 (= CSURP4512) and Anaerococcus vaginimassiliensis sp. nov. strain Marseille-P4857 (= CSURP4857) were isolated from the vagina of a French woman. The phylogenic tree, phenotypic criteria and genomic analysis described here clearly show that these two bacteria are different from previously known bacterial species with standing in nomenclature and new members of Firmicutes phylum.

Published
2020

39. Pseudoruminococcus massiliensis gen. nov., sp. nov., a new bacterium isolated from the human gut microbiota

Author

Pamela Afouda, Grégory Dubourg, Didier Raoult, Thi Tien Nguyen, Pierre-Edouard Fournier, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, taxono-genomics, 030106 microbiology, Gut flora, digestive system, Microbiology, lcsh:Infectious and parasitic diseases, taxonomy, 03 medical and health sciences, Human gut, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, lcsh:RC109-216, human microbiota, ComputingMilieux_MISCELLANEOUS, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Culturomics, biology, Human microbiome, New Specie, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 6. Clean water, 3. Good health, 030104 developmental biology, Infectious Diseases, Pseudoruminococcus massiliensis, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Taxonomy (biology), Family Ruminococcaceae, Bacteria
Abstract

Pseudoruminococcus massiliensis strain Marseille-P3876T (= CSUR P3876) is a new genus from the family Ruminococcaceae that was isolated from the gut microbiota of a healthy Senegalese man. Keywords: Culturomics, human microbiota, taxonomy, taxono-genomics, Pseudoruminococcus massiliensis

Published
2020

40. Muscular hydatidosis

Author

Petit, C., L'Ollivier, C., Mattei, J.-C., Menard, A., Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, Images in Clinical Microbiology, 030306 microbiology, serology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, hydatidosis, 03 medical and health sciences, scolex, 0302 clinical medicine, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, muscular, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 030212 general & internal medicine, Hooklets, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2020

41. Anaerosphaera massiliensis sp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy

Author

T. Takakura, Hussein Anani, J.Y. Bou Khalil, Didier Raoult, Rania Francis, Melhem Bilen, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, Anaerosphaera massiliensis, taxono-genomics, 030106 microbiology, Biology, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, fluids and secretions, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, stool, ComputingMilieux_MISCELLANEOUS, Anaerosphaera, new species, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Strain (chemistry), New Specie, culturomics, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Infectious Diseases, Culturomics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Bacteria
Abstract

Anaerosphaera massiliensis strain Marseille-P4592T (= CSURP4592T; = CCUG72452T) is a new species isolated from the stool of a 39-year-old male Pygmy from the Democratic Republic of Congo. Keywords: Anaerosphaera massiliensis, culturomics, new species, stool, taxono-genomics

Published
2020

42. Leptospirosis in French Polynesia: 11 years of surveillance data, 2007-2017

Author

Didier Musso, S. Lastère, C. Benoit de Coignac, F. Chaix, J. Formont, M. Giard, N. Bouscaren, Y. Teissier, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, medicine.medical_specialty, Epidemiology, 030106 microbiology, Population, Disease, Microbiology, law.invention, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, law, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Environmental health, Medicine, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, education, ComputingMilieux_MISCELLANEOUS, education.field_of_study, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, business.industry, Incidence (epidemiology), Public health, Zoonosis, public health/epidemiology, medicine.disease, Leptospirosis, Intensive care unit, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, leptospirosis/epidemiology, 3. Good health, zoonoses, 030104 developmental biology, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, incidence, Original Article, polynesia/epidemiology, business
Abstract

Leptospirosis is a worldwide zoonosis with higher incidence in tropical areas and is a neglected disease in the Pacific region. French Polynesia (FP) is a French overseas territory located in the South Pacific. Data on the epidemiology in FP are scarce. In this study, we describe our understanding of leptospirosis epidemiology in FP and discuss the prospects concerning this disease and its surveillance to better address preventive actions. We report 11 years of surveillance data between 1 January 2007 and 31 December 2017. Over the study period, 1356 confirmed and probable leptospirosis cases were reported. The mean annual incidence rate was 46.0 (95% confidence interval, 43.6–48.5) cases per 100 000 inhabitants. We registered 864 (63.7%) hospitalizations; of these, at least 270 (19.9%) were in the intensive care unit, and 24 patients (1.8%) died. Even if the incidence of leptospirosis is lower in FP compared to most of other Pacific countries and territories, our data confirm that the disease is highly endemic in FP. Despite all the preventive measures taken, leptospirosis remains a major public health concern in FP, thus highlighting the need to maintain intensive leptospirosis surveillance, medical staff training and provision of information to the general population. Keywords: Epidemiology, incidence, leptospirosis/epidemiology, polynesia/epidemiology, public health/epidemiology, zoonoses

Published
2018

43. History of arthropod-borne virus infections in French Polynesia

Author

Maite Aubry, Van-Mai Cao-Lormeau, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD), and Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
0301 basic medicine, chikungunya, Ross River, viruses, 030106 microbiology, French Polynesia, Dengue virus, medicine.disease_cause, Microbiology, Arbovirus, lcsh:Infectious and parasitic diseases, Dengue fever, Zika virus, 03 medical and health sciences, Ross River virus, Zika, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Chikungunya, ComputingMilieux_MISCELLANEOUS, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, biology, Transmission (medicine), Outbreak, virus diseases, biochemical phenomena, metabolism, and nutrition, medicine.disease, biology.organism_classification, Article(s) from the Special Issue on Infections in Polynesia, Virology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, dengue, 3. Good health, Pacific, 030104 developmental biology, Infectious Diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology
Abstract

In French Polynesia, arthropod-borne diseases are major public health problems. From the mid-1940s, the four serotypes of dengue virus (DENV-1 to -4) have caused 15 epidemics of variable severity. In 2013, for the first time, a sustained co-circulation of two different DENV serotypes (DENV-1 and -3) was reported. The same year, Zika virus (ZIKV) caused the largest outbreak ever recorded at that time. Severe neurologic complications in adults, including Guillain-Barré syndrome and central nervous system malformations in newborns and foeteuses, such as microcephaly, were reported, and a causal link with ZIKV infection was established. In addition to mosquito-borne transmission, the potential for perinatal, sexual and blood-transfusion transmission of ZIKV was demonstrated. In 2014, chikungunya virus (CHIKV) caused an explosive outbreak. Series of Guillain-Barré syndrome temporally associated with the CHIKV epidemic were reported. Except for DENV, ZIKV and CHIKV, no other arboviruses have been detected so far, but serologic evidence suggested the past silent circulation of Ross River virus. From May 2015 DENV-1 has been the only arbovirus transmitted in French Polynesia, but the reemergence of DENV-2 is highly expected since the detection of two autochthonous cases of DENV-2 infection in June 2018. Keywords: Arbovirus, chikungunya, dengue, French Polynesia, Pacific, Ross River, Zika

Published
2018

44. Vaginisenegalia massiliensis gen. nov., sp. nov., a new bacterium isolated from the vagina flora and its taxono-genomic description

Author

Nicholas Armstrong, Didier Raoult, Cheikh Sokhna, Pierre-Edouard Fournier, J.-C. Lagier, Ndeye Safietou Fall, A. Fadlane, Florence Fenollar, Cheikh Ibrahima Lo, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)

Subjects
0301 basic medicine, Flora, Phylum Firmicutes, 030106 microbiology, sp. nov, Biology, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genus, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, taxono-genomic, Nomenclature, Genome size, ComputingMilieux_MISCELLANEOUS, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Culturomics, Strain (biology), New Specie, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Infectious Diseases, vagina, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Vaginisenegalia massiliensis gen. nov, Bacteria
Abstract

Strain Marseille-P5643T was isolated from a vaginal sample of a healthy Senegalese woman. It is an anaerobic Gram-negative, rod-shaped bacterium. Strain Marseille-P5643T exhibits 93.7% similarity levels with the Facklamia hominis strain ATCC 700628T, the phylogenetically closest related species with standing in nomenclature. The draft genome size of strain Marseille-P5643T is 1.79 Mb with 39.0 mol% of G+C content. We propose here the creation of Vaginisenegalia massiliensis gen. nov., sp. nov., as a new bacterial genus from the phylum Firmicutes. Keywords: Culturomics, sp. nov, taxono-genomic, vagina, Vaginisenegalia massiliensis gen. nov.

Published
2019

45. New approaches in the systematics of rickettsiae

Author

A.A. Skiba, Pierre-Edouard Fournier, A.S. Gumenuk, N.N. Pozdnichenko, Shpynov Sn, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
0301 basic medicine, Systematics, Computational biology, Microbiology, Genome, Homology (biology), Rickettsiaceae, rickettsioses, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, rickettsiae, lcsh:RC109-216, systematics, Gene, Arthropods, genome, ComputingMilieux_MISCELLANEOUS, genomosystematics, biology, biology.organism_classification, Rickettsia africae, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, virulence, 030104 developmental biology, Infectious Diseases, Candidatus, Original Article, epidemiology, ecology, Rickettsiales, formal order analysis
Abstract

The development of a formal order analysis (FOA) allowed constructing a classification of 49 genomes of Rickettsiaceae family representatives. Recently FOA has been extended with new tools—‘Map of genes,’ ‘Matrix of similarity’ and ‘Locality-sensitive hashing’—for a more in-depth study of the structure of rickettsial genomes. The new classification confirmed and supplemented the previously constructed one by determining the position of Rickettsia africae str. ESF-5, R. heilongjiangensis 054, R. monacensis str. IrR/Munich, R. montanensis str. OSU 85-930, R. raoultii str. Khabarovsk, R. rhipicephali str. 3-7-female6-CWPP and Rickettsiales bacterium str. Ac37b. The ‘Map of genes’ demonstrated the complete genomes and their components in a graphical form. The ‘Matrix of similarity’ was applied for an in-depth classification to a subtaxonomic category of the strain within the species R. rickettsii (11 strains) and R. prowazekii (ten strains). The ‘Matrix of similarity’ determines the degree of homology of complete genomes by pairwise comparison of their components and identification of those being identical and similar in the arrangement of nucleotides. A new genomosystematics approach is proposed for the study of complete genomes and their components through the development and application of FOA tools. Its applications include the development of principles for the classification of microorganisms, based on the analysis of complete genomes and their annotations. This approach may help in the taxonomic classification and characterization of some Candidatus Rickettsia spp. that are found in large numbers in arthropods worldwide. Keywords: Arthropods, ecology, epidemiology, formal order analysis, genome, genomosystematics, rickettsiae, rickettsioses, systematics, virulence

Published
2017

46. ' Streptomyces massilialgeriensis ' sp. nov., a new bacterial species isolated from an extremely saline soil collected from the dry lake of Ank el Djamel in Algeria

Author

Didier Raoult, Saber Khelaifia, C. E. Djaballah, M. Kitouni, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48, INSB-INSB-Centre National de la Recherche Scientifique (CNRS), Université Mentouri Constantine [Algérie] (UMC), Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Université frères Mentouri Constantine I (UMC), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), and HAL AMU, Administrateur

Subjects
0301 basic medicine, Soil salinity, taxono-genomics, 030106 microbiology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, Streptomyces, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Genus, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Botany, “Streptomyces massilialgeriensis”, lcsh:RC109-216, Culturomics, biology, Strain (biology), New Specie, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, dry lake, 030104 developmental biology, Infectious Diseases, "Streptomyces massilialgeriensis", saline soil, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Abstract

We report here the main characteristics of “Streptomyces massilialgeriensis” strain S35T (CSUR = P3927), a new bacterial species within the Streptomyces genus, isolated from an extremely saline soil sample collected from the site of Garaet Ank Djemel in the Wilaya of Oum El Bouaghi, Algeria. Keywords: Culturomics, dry lake, saline soil, “Streptomyces massilialgeriensis”, taxono-genomics

Published
2018

47. Genome sequence and description of Bacteroides bouchesdurhonensis sp. nov., a new anaerobic bacterium isolated from the human gut

Author

Anthony Levasseur, Saber Khelaifia, S. Ndongo, Pierre-Edouard Fournier, Mamadou Lamine Tall, Didier Raoult, Issa Isaac Ngom, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA), Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
Firmicutes, Gut flora, digestive system, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Human gut, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lcsh:RC109-216, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Whole genome sequencing, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, biology, 030306 microbiology, Phylum, Strain (biology), food and beverages, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 6. Clean water, Infectious Diseases, Culturomics, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Bacteroides
Abstract

Bacteroides bouchesdurhonensis sp. nov., strain Marseille-P2653T (= CSUR; P2653=DSM103120) is a new bacterial species belonging to the Firmicutes phylum in the family Bacteroidaceae that was isolated from the human gut microbiota. Keywords: Anaerobic bacterium, Bacteroides bouchesdurhonensissp. nov., culturomics, gut microbiota, taxonogenomics

Published
2019

48. Corrigendum to ‘'Mediterranea massiliensis' gen. nov., sp. nov., a new human-associated bacteria isolated from the right and left colon lavage of a 58-year-old patient’

Author

Didier Raoult, Pierre-Edouard Fournier, Saber Khelaifia, D. Ricaboni, M. Mailhe, A. Benezech, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Department of Biomedical and Clinical Sciences, ASST Fatebenefratelli Sacco, Luigi Sacco Hospital, University of Milan, Milan, Italy, Assistance Publique - Hôpitaux de Marseille (APHM), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Università degli Studi di Milano = University of Milan (UNIMI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)

Subjects
[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, Culturomics, 030306 microbiology, New Species, Mediterranea massiliensis, taxonogenomics, Biology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, taxonomy, 03 medical and health sciences, Infectious Diseases, Left colon, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, genomics, Associated bacteria, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, Corrigendum, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

We report here the main characteristics of ‘Mediterranea massiliensis’ strain Marseille-P2645T (CSURP2645) that was isolated from stored samples of gut.

Published
2019

49. Lactimicrobium massiliense gen. nov., sp. nov.; Anaerolactibacter massiliensis gen. nov., sp. nov.; Galactobacillus timonensis gen. nov., sp. nov. and Acidipropionibacterium timonense sp. nov. isolated from breast milk from healthy breastfeeding African women

Author

Nicholas Armstrong, V. Brevaut, Pierre-Edouard Fournier, Aminata Camara, Yanis Roussel, Didier Raoult, Jeremy Delerce, Mahamadou Ali Thera, M. Million, C. Des Robert, Awa Diop, Edmond Kuete, Amadou Hamidou Togo, Salimata Konate, Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
0301 basic medicine, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Strain (biology), 030106 microbiology, Breastfeeding, Breast milk, Biology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Microbiology, lcsh:Infectious and parasitic diseases, 3. Good health, 03 medical and health sciences, 030104 developmental biology, Infectious Diseases, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, Culturomics, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Genus, Taxonogenomics: Genome of a Known Organism, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, lcsh:RC109-216, Human breast milk, ComputingMilieux_MISCELLANEOUS
Abstract

Four strains isolated by microbial culturomics from breast milk of healthy mothers from Mali were not identified and characterized by taxono-genomics. This led us to propose the new genera and species Lactimicrobium massiliense, Anaerolactibacter massiliensis and Galactobacillus timonensis containing type strain Marseille-P4301T (CSUR P4301T), Marseille-P4302T (CSUR P4302T) and Marseille-P4641T (CSUR P4641T), respectively. The strain Marseille-P4482 represents a novel species, Acidipropionibacterium timonense, in a previously known genus with type strain being Marseille-P4482T (CSUR P4482T). Keywords: Culturomics, human breast milk, microbiome, microbiota, taxono-genomics

Published
2019

50. Corrigendum to '‘Bacteroides mediterraneensis’ sp. nov., a new human-associated bacterium isolated from ileum specimen'

Author

Pierre-Edouard Fournier, Véronique Vitton, M. Mailhe, Saber Khelaifia, D. Ricaboni, Didier Raoult, Vecteurs - Infections tropicales et méditerranéennes (VITROME), Institut de Recherche Biomédicale des Armées (IRBA)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Microbes évolution phylogénie et infections (MEPHI), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
New Species, Ileum, Biology, Microbiology, Bacteroides mediterraneensis, taxonomy, 03 medical and health sciences, [SDV.MHEP.CSC]Life Sciences [q-bio]/Human health and pathology/Cardiology and cardiovascular system, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, genomics, medicine, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, 0303 health sciences, 030306 microbiology, food and beverages, culturomics, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Infectious Diseases, medicine.anatomical_structure, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Corrigendum, Bacteria
Abstract

We report here the main characteristics of 'Bacteroides mediterraneensis' strain Marseille-P2644(T) (CSURP2644) that was isolated from the stored samples of gut.

Published
2019

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