25 results on '"J.Y. Bou Khalil"'
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2. Anaerosphaera massiliensis sp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy
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T. Takakura, R. Francis, H. Anani, M. Bilen, D. Raoult, and J.Y. Bou Khalil
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Infectious and parasitic diseases ,RC109-216 - 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
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- 2020
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3. ‘Massilibacteroïdes vaginae’ gen. nov., sp. nov., a new genus within the family of Bacteroïdaceae isolated from a patient with vaginosis
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J. Jneid, J.Y. Bou Khalil, S. Aherfi, C. Blanc-Tailleur, D. Raoult, B. La Scola, and I. Pagnier
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Infectious and parasitic diseases ,RC109-216 - Abstract
‘Massilibacteroïdes vaginae’ sp. nov. strain MV12T is the type strain of ‘Massilibacteroïdes’ gen. nov., a new genus within the family of Porphyromonadaceae. This strain was isolated in Marseille from a patient with vaginosis. ‘Massilibacteroïdes vaginae’ is a Gram-negative, aero-anaerobic bipolar bacillus. Here we describe the phenotypic characteristics and complete genome sequence of this bacterium. The EMBL accession number is FXDJ00000000 (FXDJ01000001–FXDJ01000009), and its genome consists of nine scaffolds. The strain was deposited in two culture collections under the numbers CSUR P1477 and DSM 100704. Keywords: Bacterial vaginosis, culturomics, genome, Massilibacteroïdes vaginae, taxonogenomics
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- 2018
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4. Clostridium transplantifaecale sp. nov., a new bacterium isolated from patient with recurrent Clostridium difficile infection
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E.K. Yimagou, M.L. Tall, J.P. Baudoin, D. Raoult, and J.Y. Bou Khalil
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Infectious and parasitic diseases ,RC109-216 - Abstract
Clostridium transplantifaecale strain Marseille-P8228T (= CSURP8228) is a new species isolated from a patient with recurrent Clostridium difficile infection. Keywords: Clostridium transplantifaecale, culturomics, new species, stool, taxono-genomics
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- 2019
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5. Dorea phocaeensis sp. nov., a new bacterium isolated from the stool of a healthy 29-year-old male
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T. Takakura, R. Francis, H. Anani, S. Naud, D. Raoult, and J.Y. Bou Khalil
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Infectious and parasitic diseases ,RC109-216 - Abstract
Dorea phocaeensis strain Marseille-P4003T (= CSURP4003T; = CCUG71359T) is a new species isolated from the stool of a healthy 29-year-old male from France. Keywords: Culturomics, Dorea phocaeensis, taxono-genomics
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- 2019
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6. Prevotella marseillensis sp. nov., a new bacterium isolated from a patient with recurrent Clostridium difficile infection
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E. Kuete Yimagou, F. Mekhalif, M. Lamine Tall, J.P. Baudoin, D. Raoult, and J.Y. Bou Khalil
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Infectious and parasitic diseases ,RC109-216 - Abstract
Prevotella marseillensis strain Marseille-P8229T (= CSURP8229) is a new species isolated from a patient with recurrent Clostridium difficile infection. It is an anaerobic, non-motile, non-spore-forming Gram-negative coccobacillus isolated from the stool of patient with recurrent Clostridium difficile infection in Marseille. We present herein its phenotypic description together with MALDI-TOF mass spectrometry analysis and genome sequencing and comparison. The genome of P. marseillensis is 4.1607 Mbp long with 45.80 mol% of G+C content, and it contains 3078 protein-coding genes. Keywords: Culturomics, New species, Prevotella marseillensis sp. nov., Stool, Taxono-genomics
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- 2019
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7. Enterobacter timonensis sp. nov., a new bacterium isolated from a fresh human stool specimen
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T. Takakura, H. Anani, A. Fadlane, A. Fontanini, D. Raoult, and J.Y. Bou Khalil
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Infectious and parasitic diseases ,RC109-216 - Abstract
Enterobacter timonensis strain mt20T (= CSUR P2201T, = DSM101775T) is a new species isolated from a fresh human stool specimen. Keywords: Culturomics, Enterobacter timonensis, Human gut, New species, Taxonogenomics
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- 2019
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8. Enterococcus mediterraneensis sp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy
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T. Takakura, R. Francis, H. Anani, M. Bilen, D. Raoult, and J.Y. Bou Khalil
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Infectious and parasitic diseases ,RC109-216 - Abstract
Enterococcus mediterraneensis strain Marseille-P4358T (= CSURP4358T) is a new species isolated from the stool of a 39-year-old male Pygmy from the Democratic Republic of Congo. Keywords: Culturomics, Enterococcus mediterraneensis, taxono-genomics
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- 2019
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9. Urinicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from a human urine sample from a 7-year-old boy hospitalized for dental care
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E.K. Yimagou, H. Anani, A. Yacouba, I. Hasni, J.-P. Baudoin, D. Raoult, and J.Y. Bou Khalil
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Infectious and parasitic diseases ,RC109-216 - Abstract
Urinicoccus massiliensis strain Marseille-P1992T (= CSURP1992 = DSM100581) is a species of a new genus isolated from human urine. Keywords: Culturomics, new species, taxonogenomics, urine, Urinicoccus massiliensis
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- 2019
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10. Acidaminococcus provencensis sp. nov., a new bacterium isolated from a fresh human stool specimen
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T. Takakura, H. Anani, A. Fadlane, A. Fontanini, D. Raoult, and J.Y. Bou Khalil
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Infectious and parasitic diseases ,RC109-216 - Abstract
Acidaminococcus provencensis strain Marseille-P4266T (= CSURP4266T) is a new species isolated from a fresh human stool specimen. Keywords: Acidaminococcus provencensis, Culturomics, Microbiota, New species, Taxonogenomics, TM4000, Stool
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- 2019
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11. Selenomonas felix sp. nov., a new bacterium isolated from human sputum
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E. Kuete, M.D. Mbogning Fonkou, F. Mekhalif, H. Anani, J.-P. Baudoin, D. Raoult, and J.Y. Bou Khalil
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Infectious and parasitic diseases ,RC109-216 - Abstract
Selenomonas felix strain Marseille-P3560T (=CSURP3560) is a new species isolated from human sputum. Keywords: Culturomics, new species, Selenomonas felix, sputum, taxonogenomics
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- 2019
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12. Brachybacterium timonense sp. nov., a new bacterium isolated from human sputum
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E. Kuete, M.D. Mbogning Fonkou, F. Mekhalif, H. Anani, J.-P. Baudoin, D. Raoult, and J.Y. Bou Khalil
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Infectious and parasitic diseases ,RC109-216 - Abstract
Brachybacterium timonense strain Marseille-P4339T (=CSURP4339, =CECT9821) is a new species isolated from human sputum. Keywords: Brachybacterium timonense, culturomics, new species, sputum, taxonogenomics
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- 2019
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13. Virgibacillus ndiopensis sp. nov., a new halophilic bacterium isolated from the stool of a healthy 11-year-old boy
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R. Francis, H. Anani, A. Fontanini, P.E. Fournier, B.L.A. Scola, D. Raoult, and J.Y. Bou Khalil
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Infectious and parasitic diseases ,RC109-216 - Abstract
Virgibacillus ndiopensis strain Marseille-P3835T (= CSURP3835T; = CCUG70388T) is a new specie isolated from the stool of a healthy 11-year-old boy from N'Diop, Senegal. Keywords: Culturomics, taxonogenomics, Virgibacillus ndiopensis
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- 2019
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14. Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses
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Yannick Gueguen, J. de Lorgeril, Samuel Dupont, C. Salmeron, G. Tanguy, Caroline Montagnani, J.Y. Bou Khalil, Jean-Christophe Auguet, Jean-Michel Escoubas, Bruno Petton, B. La Scola, Eve Toulza, A. Lokmer, Christelle Desnues, Guillaume Mitta, David Pecqueur, Erwan Corre, Laure Guillou, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Éco-Anthropologie (EA), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Observatoire océanologique de Banyuls (OOB), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), ECOlogy of MArine Plankton (ECOMAP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), 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), The present study was supported by: the DHOF program of the UMR5244/IHPE (http://ihpe.univ-perp.fr/en/ihpe-transversal-holobiont/), the Ifremer project HémoMicrobiote, EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future (ANR-10-INBS-02), the ANR projects DECIPHER (ANR-14-CE19–0023) and ENVICOPAS (ANR-15-CE35–0004), the EU funded project VIVALDI (H2020 program, n°678589), by Ifremer, CNRS, Université de Montpellier, Université de Perpignan via Domitia, by the IHU Méditerranée Infection, Marseille, France, by the French Government under the «Investissements d’avenir» program (reference: Méditerranée Infection 10-IAHU-03) and by the Région Provence-Alpes-Côte d’Azur and by the European funding FEDER PRIMI. This study is set within the framework of the 'Laboratoires d’Excellences (LABEX)' TULIP (ANR-10-LABX-41)., ANR-10-INBS-0002,EMBRC-France,CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES(2010), ANR-14-CE19-0023,DECIPHER,Déchiffrage des maladies multifactorielles: cas des mortalités de l'huître(2014), ANR-15-CE35-0004,ENVICOPAS,Impact des changements environnementaux sur les organismes pathogènes dans les écosystèmes côtiers(2015), ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), European Project: 678589,H2020,H2020-SFS-2015-2,VIVALDI(2016), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Éco-Anthropologie (EAE), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Adaptation et diversité en milieu marin (AD2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut d’Électronique, de Microélectronique et de Nanotechnologie (IEMN) - UMR 8520 (IEMN), Ecole Centrale de Lille-Institut supérieur de l'électronique et du numérique (ISEN)-Université de Valenciennes et du Hainaut-Cambrésis (UVHC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université Polytechnique Hauts-de-France (UPHF), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB)-Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2, Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Génome, populations, interactions, adaptation (GPIA), Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Montpellier 2 - Sciences et Techniques (UM2), Parasitologie fonctionnelle et évolutive (PFE), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Radiopathologie et Thérapies Expérimentales [IRSN, Fontenay-aux-Roses] (PRP-HOM - SRBE), Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
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Oyster ,animal structures ,Early-life microbiota ,lcsh:QR1-502 ,Zoology ,medicine.disease_cause ,Within-host ecosystem ,lcsh:Microbiology ,03 medical and health sciences ,biology.animal ,medicine ,Trans-kingdom interactions ,Human virome ,Microbiome ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,Ecological niche ,0303 health sciences ,lcsh:Veterinary medicine ,biology ,030306 microbiology ,Host (biology) ,Oyster genetic background ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,fungi ,Protist ,General Medicine ,Pacific oyster ,biology.organism_classification ,Transplantation ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,[SDE]Environmental Sciences ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Crassostrea gigas ,lcsh:SF600-1100 ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Acln ,Hemolymph microbiota dynamics ,Research Article - Abstract
Background The impact of the microbiota on host fitness has so far mainly been demonstrated for the bacterial microbiome. We know much less about host-associated protist and viral communities, largely due to technical issues. However, all microorganisms within a microbiome potentially interact with each other as well as with the host and the environment, therefore likely affecting the host health. Results We set out to explore how environmental and host factors shape the composition and diversity of bacterial, protist and viral microbial communities in the Pacific oyster hemolymph, both in health and disease. To do so, five oyster families differing in susceptibility to the Pacific oyster mortality syndrome were reared in hatchery and transplanted into a natural environment either before or during a disease outbreak. Using metabarcoding and shotgun metagenomics, we demonstrate that hemolymph can be considered as an ecological niche hosting bacterial, protist and viral communities, each of them shaped by different factors and distinct from the corresponding communities in the surrounding seawater. Overall, we found that hemolymph microbiota is more strongly shaped by the environment than by host genetic background. Co-occurrence network analyses suggest a disruption of the microbial network after transplantation into natural environment during both non-infectious and infectious periods. Whereas we could not identify a common microbial community signature for healthy animals, OsHV-1 μVar virus dominated the hemolymph virome during the disease outbreak, without significant modifications of other microbiota components. Conclusion Our study shows that oyster hemolymph is a complex ecosystem containing diverse bacteria, protists and viruses, whose composition and dynamics are primarily determined by the environment. However, all of these are also shaped by oyster genetic backgrounds, indicating they indeed interact with the oyster host and are therefore not only of transient character. Although it seems that the three microbiome components respond independently to environmental conditions, better characterization of hemolymph-associated viruses could change this picture.
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- 2020
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15. Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation
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J.Y. Bou Khalil, G. Haddad, Rita Zgheib, Ahmad Ibrahim, Didier Raoult, A. Rajaonison, Fadi Bittar, M. Maatouk, 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), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)
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Microbiology (medical) ,Saccharibacteria ,Physiology ,Computational biology ,Biology ,Polymerase Chain Reaction ,Microbiology ,Genome ,Minimicrobia ,[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 ,Genetics ,Humans ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,Microbiome ,protocol ,Protocol (object-oriented programming) ,Schaalia odontolytica ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,Bacteria ,General Immunology and Microbiology ,Ecology ,Obligate ,Phylum ,Microbiota ,candidate phyla radiation ,Cell Biology ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,Coculture Techniques ,QR1-502 ,Culture Media ,Infectious Diseases ,Metagenomics ,Actinomycetaceae ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Candidatus ,coculture ,real-time PCR ,Research Article - Abstract
The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, Candidate Phyla Radiation or CPR have been recognised as representing a large proportion of the microbial kingdom (> 26%). CPR are characterised by their obligate symbiotic or exo-parasitic activity with other microbial hosts, mainly bacteria. Currently, isolating CPR is still considered challenging for microbiologists. The idea of this study was to develop an adapted protocol for the co-culture of CPR with a suitable bacterial host. Based on various sputa, we tried to purify CPR (Saccharibacteria members) and to cultivate them with pure hosts. This protocol was monitored by real-time PCR quantification using a specific system for Saccharibacteria designed in this study, as well as by electron microscopy and sequencing. We succeeded in co-culturing and sequencing a complete genome of two new Saccharibacteria species: Candidatus Minimicrobia naudis and Candidatus Minimicrobia vallesae. In addition, we noticed a decrease in the Ct number of Saccharibacteria, and a significant multiplication through their physical association with Schaalia odontolytica strains in the enriched medium that we developed. This work may help bridge gaps in the genomic database by providing new CPR members and, in the future, their currently unknown characteristics may be revealed.IMPORTANCEIn this study, the first real-time PCR system has been developed. This technique is able to quantify specifically Saccharibacteria members in any sample of interest in order to investigate their prevalence. In addition, another easy, specific and sensitive protocol has been developed to maintain the viability of Saccharibacteria cells in an enriched medium with their bacterial host. The use of this protocol subsequently facilitates studying the phenotypic characteristics of CPR and their physical interactions with bacterial species, as well as the sequencing of new genomes to improve the current database.
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- 2021
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16. Parabacteroides bouchesdurhonensis sp. nov., a new bacterium isolated from the stool of a healthy adult
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Edmond Kuete Yimagou, Issa Isaac Ngom, Didier Raoult, Mamadou Lamine Tall, J.Y. Bou Khalil, Jean-Pierre Baudoin, Niokhor Dione, 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 Hospitalier Universitaire Méditerranée Infection (IHU Marseille)
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0301 basic medicine ,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 ,new species ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,Culturomics ,Strain (chemistry) ,digestive, oral, and skin physiology ,New Specie ,Parabacteroides ,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 ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,human activities ,Bacteria ,Parabacteroides bouchesdurhonensis - Abstract
Parabacteroides bouchesdurhonensis strain Marseille-P3763T (= CSURP3763) is a new species isolated from the stool of a heathy adult. Keywords: Culturomics, new species, Parabacteroides bouchesdurhonensis, stool, taxono-genomics
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- 2020
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17. Enterobacter timonensis sp. nov., a new bacterium isolated from a fresh human stool specimen
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Hussein Anani, Anthony Fontanini, J.Y. Bou Khalil, Didier Raoult, A. Fadlane, T. Takakura, Microbes évolution phylogénie et infections (MEPHI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
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0301 basic medicine ,030106 microbiology ,taxonogenomics ,Stool specimen ,Biology ,Microbiology ,Enterobacter timonensis ,Human gut ,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 ,ComputingMilieux_MISCELLANEOUS ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,Culturomics ,Strain (chemistry) ,digestive, oral, and skin physiology ,New Specie ,biology.organism_classification ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,New species ,030104 developmental biology ,Infectious Diseases ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Bacteria - Abstract
Enterobacter timonensis strain mt20T (= CSUR P2201T, = DSM101775T) is a new species isolated from a fresh human stool specimen. Keywords: Culturomics, Enterobacter timonensis, Human gut, New species, Taxonogenomics
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- 2019
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18. Enterococcus mediterraneensis sp. nov., a new bacterium isolated from the stool of a 39-year-old Pygmy
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J.Y. Bou Khalil, Rania Francis, Melhem Bilen, Hussein Anani, T. Takakura, Didier Raoult, Microbes évolution phylogénie et infections (MEPHI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
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Enterococcus mediterraneensis ,0301 basic medicine ,taxono-genomics ,030106 microbiology ,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 ,lcsh:RC109-216 ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,ComputingMilieux_MISCELLANEOUS ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,Culturomics ,biology ,Strain (chemistry) ,biochemical phenomena, metabolism, and nutrition ,New Specie ,biology.organism_classification ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,6. Clean water ,030104 developmental biology ,Infectious Diseases ,Enterococcus ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Bacteria - Abstract
Enterococcus mediterraneensis strain Marseille-P4358T (= CSURP4358T) is a new species isolated from the stool of a 39-year-old male Pygmy from the Democratic Republic of Congo. Keywords: Culturomics, Enterococcus mediterraneensis, taxono-genomics
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- 2019
- Full Text
- View/download PDF
19. Acidaminococcus provencensis sp. nov., a new bacterium isolated from a fresh human stool specimen
- Author
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Hussein Anani, Didier Raoult, A. Fadlane, T. Takakura, J.Y. Bou Khalil, Anthony Fontanini, 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), and Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU)
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0301 basic medicine ,Acidaminococcus provencensis ,030106 microbiology ,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 ,[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 ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,Culturomics ,biology ,Strain (chemistry) ,Taxonogenomics ,Microbiota ,digestive, oral, and skin physiology ,New Specie ,biology.organism_classification ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,3. Good health ,New species ,030104 developmental biology ,Infectious Diseases ,Stool ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Acidaminococcus ,TM4000 ,Bacteria - Abstract
Acidaminococcus provencensis strain Marseille-P4266T (= CSURP4266T) is a new species isolated from a fresh human stool specimen. Keywords: Acidaminococcus provencensis, Culturomics, Microbiota, New species, Taxonogenomics, TM4000, Stool
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- 2019
- Full Text
- View/download PDF
20. Clostridium transplantifaecale sp. nov., a new bacterium isolated from patient with recurrent Clostridium difficile infection
- Author
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J.Y. Bou Khalil, Didier Raoult, Mamadou Lamine Tall, Jean-Pierre Baudoin, Edmond Kuete Yimagou, Microbes évolution phylogénie et infections (MEPHI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0301 basic medicine ,taxono-genomics ,030106 microbiology ,Biology ,Microbiology ,lcsh:Infectious and parasitic diseases ,03 medical and health sciences ,Clostridium ,[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 ,stool ,ComputingMilieux_MISCELLANEOUS ,new species ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,Strain (chemistry) ,Clostridium difficile ,New Specie ,culturomics ,biology.organism_classification ,[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 ,Clostridium transplantifaecale ,Bacteria - Abstract
Clostridium transplantifaecale strain Marseille-P8228T (= CSURP8228) is a new species isolated from a patient with recurrent Clostridium difficile infection. Keywords: Clostridium transplantifaecale, culturomics, new species, stool, taxono-genomics
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- 2019
- Full Text
- View/download PDF
21. Virgibacillus ndiopensis sp. nov., a new halophilic bacterium isolated from the stool of a healthy 11-year-old boy
- Author
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Didier Raoult, Anthony Fontanini, Rania Francis, Bernard La Scola, Pierre-Edouard Fournier, Hussein Anani, J.Y. Bou Khalil, 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), 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 pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)
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0301 basic medicine ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,biology ,Strain (chemistry) ,030106 microbiology ,New Specie ,biology.organism_classification ,Microbiology ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,Halophile ,3. Good health ,lcsh:Infectious and parasitic diseases ,03 medical and health sciences ,030104 developmental biology ,Infectious Diseases ,Culturomics ,[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 ,Virgibacillus ,lcsh:RC109-216 ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,Bacteria ,ComputingMilieux_MISCELLANEOUS - Abstract
Virgibacillus ndiopensis strain Marseille-P3835T (= CSURP3835T; = CCUG70388T) is a new specie isolated from the stool of a healthy 11-year-old boy from N'Diop, Senegal. Keywords: Culturomics, taxonogenomics, Virgibacillus ndiopensis
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- 2019
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- View/download PDF
22. 'Massilibacteroides vaginae' gen. nov., sp. nov., a new genus within the family of Bacteroidaceae isolated from a patient with vaginosis
- Author
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Didier Raoult, Sarah Aherfi, Joanne Jneid, Isabelle Pagnier, Caroline Blanc-Tailleur, B. La Scola, J.Y. Bou Khalil, 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), 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), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
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0301 basic medicine ,Porphyromonadaceae ,taxonogenomics ,Microbiology ,lcsh:Infectious and parasitic diseases ,03 medical and health sciences ,Genus ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,lcsh:RC109-216 ,Massilibacteroides vaginae ,Bacteroidaceae ,genome ,Bacillus (shape) ,Whole genome sequencing ,biology ,Accession number (library science) ,Strain (biology) ,Bacterial vaginosis ,culturomics ,biology.organism_classification ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,3. Good health ,030104 developmental biology ,Infectious Diseases ,Culturomics - Abstract
‘Massilibacteroïdes vaginae’ sp. nov. strain MV12T is the type strain of ‘Massilibacteroïdes’ gen. nov., a new genus within the family of Porphyromonadaceae. This strain was isolated in Marseille from a patient with vaginosis. ‘Massilibacteroïdes vaginae’ is a Gram-negative, aero-anaerobic bipolar bacillus. Here we describe the phenotypic characteristics and complete genome sequence of this bacterium. The EMBL accession number is FXDJ00000000 (FXDJ01000001–FXDJ01000009), and its genome consists of nine scaffolds. The strain was deposited in two culture collections under the numbers CSUR P1477 and DSM 100704. Keywords: Bacterial vaginosis, culturomics, genome, Massilibacteroïdes vaginae, taxonogenomics
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- 2018
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- View/download PDF
23. Urinicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from a human urine sample from a 7-year-old boy hospitalized for dental care
- Author
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Abdourahamane Yacouba, Hussein Anani, Edmond Kuete Yimagou, J.Y. Bou Khalil, Issam Hasni, Didier Raoult, Jean-Pierre Baudoin, Microbes évolution phylogénie et infections (MEPHI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0301 basic medicine ,030106 microbiology ,taxonogenomics ,Urine ,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 ,ComputingMilieux_MISCELLANEOUS ,new species ,[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 ,Dental care ,urine ,3. Good health ,030104 developmental biology ,Infectious Diseases ,Urinicoccus massiliensis ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Urine sample ,human activities ,Bacteria - Abstract
Urinicoccus massiliensis strain Marseille-P1992T (= CSURP1992 = DSM100581) is a species of a new genus isolated from human urine. Keywords: Culturomics, new species, taxonogenomics, urine, Urinicoccus massiliensis
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- 2019
- Full Text
- View/download PDF
24. Dorea phocaeensis sp. nov., a new bacterium isolated from the stool of a healthy 29-year-old male
- Author
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S. Naud, Didier Raoult, Hussein Anani, T. Takakura, J.Y. Bou Khalil, Rania Francis, Microbes évolution phylogénie et infections (MEPHI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0301 basic medicine ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,Culturomics ,Strain (chemistry) ,taxono-genomics ,Dorea phocaeensis ,030106 microbiology ,New Specie ,Biology ,biology.organism_classification ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,Microbiology ,lcsh:Infectious and parasitic diseases ,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 ,[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,lcsh:RC109-216 ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,ComputingMilieux_MISCELLANEOUS ,Bacteria - Abstract
Dorea phocaeensis strain Marseille-P4003T (= CSURP4003T; = CCUG71359T) is a new species isolated from the stool of a healthy 29-year-old male from France. Keywords: Culturomics, Dorea phocaeensis, taxono-genomics
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- 2019
- Full Text
- View/download PDF
25. Prevotella marseillensis sp. nov., a new bacterium isolated from a patient with recurrent Clostridium difficile infection
- Author
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F. Mekhalif, E. Kuete Yimagou, M. Lamine Tall, Didier Raoult, J.Y. Bou Khalil, Jean-Pierre Baudoin, Microbes évolution phylogénie et infections (MEPHI), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0301 basic medicine ,030106 microbiology ,Taxono-genomics ,Microbiology ,Genome ,DNA sequencing ,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 ,Prevotella ,lcsh:RC109-216 ,[SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology ,Gene ,ComputingMilieux_MISCELLANEOUS ,[SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases ,Culturomics ,Prevotella marseillensis sp. nov ,biology ,New Specie ,Clostridium difficile ,biology.organism_classification ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,New species ,3. Good health ,030104 developmental biology ,Infectious Diseases ,Stool ,Coccobacillus ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Bacteria - Abstract
Prevotella marseillensis strain Marseille-P8229T (= CSURP8229) is a new species isolated from a patient with recurrent Clostridium difficile infection. It is an anaerobic, non-motile, non-spore-forming Gram-negative coccobacillus isolated from the stool of patient with recurrent Clostridium difficile infection in Marseille. We present herein its phenotypic description together with MALDI-TOF mass spectrometry analysis and genome sequencing and comparison. The genome of P. marseillensis is 4.1607 Mbp long with 45.80 mol% of G+C content, and it contains 3078 protein-coding genes. Keywords: Culturomics, New species, Prevotella marseillensis sp. nov., Stool, Taxono-genomics
- Published
- 2019
- Full Text
- View/download PDF
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