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578 results on '"taxonogenomics"'

301. ‘Bacteroides cutis,’ a new bacterial species isolated from human skin.

Author

Belkacemi, S., Cassir, N., Delerce, J., Cadoret, F., and La Scola, B.

Subjects
*BACTEROIDES, *SKIN microbiology, *OLDER men, *BACTERIAL cultures, *DISEASES in older people
Abstract

We report the main characteristics of ‘Bacteroides cutis’ sp. nov., strain Marseille-P4118 T (= CSUR P4118), a new species within the genus Bacteroides . This strain was isolated from a skin sample of a 75-year-old man from Marseille. [ABSTRACT FROM AUTHOR]

Published
2018
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302. Non-contiguous finished genome sequence and description of Kallipyga massiliensis gen. nov., sp. nov., a new member of the family Clostridiales Incertae Sedis XI

Author

Carine Couderc, Perrine Hugon, Didier Raoult, Dhamodharan Ramasamy, Catherine Robert, and Pierre-Edouard Fournier

Subjects
Whole genome sequencing, Genetics, Clostridiales, taxonogenomics, Kallipyga massiliensis, culturomics, Ribosomal RNA, Biology, Genome, Incertae sedis, Short Genome Reports, Type species, Culturomics, Genus, genome
Abstract

Kallipyga massiliensis strain ph2(T) is the type strain of Kallipyga massiliensis gen. nov., sp. nov., the type species of the new genus Kallipyga within the family Clostridiales Incertae Sedis XI. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. K. massiliensis is an obligate anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,770,679 bp long genome (1 chromosome but no plasmid) contains 1,575 protein-coding and 50 RNA genes, including 4 rRNA genes.

Published
2013

303. Noncontiguous finished genome sequence and description of

Author

P, Afouda, S, Ndongo, S, Khelaifia, N, Labas, F, Cadoret, F, Di Pinto, J, Delerce, D, Raoult, and M, Million

Subjects
gut microbiota, New Species, Clostridium difficile, taxonogenomics, culturomics, Prevotella phocaeensis
Abstract

Prevotella phocaeensis sp. nov. strain SN19T (= DSM 103364) is a new species isolated from the gut microbiota of patient with colitis due to Clostridium difficile. Strain SN19T is Gram-negative rod-shaped bacteria, strictly anaerobic, nonmotile and non–endospore forming. The predominance fatty acid is hexadecanoic acid. Its 16S rRNA showed a 97.70% sequence identity with its phylogenetically closest species, Prevotella oralis. The genome is 2 922 117 bp long and contains 2486 predicted genes including 56 RNA genes.

Published
2016

304. Genome sequence and description of

Author

N, Mathlouthi, S I, Traore, T, Cimmino, S, Khelaifia, T T, Nguyen, F, Cadoret, C, Couderc, D, Raoult, and J-M, Rolain

Subjects
Culturomics, Original Article, Mobilicoccus massiliensis, taxonogenomics, genome, kwashiorkor
Abstract

Mobilicoccus massiliensis strain SIT2 (= CSUR P1306 = DSM 29065) is a new type strain of Mobilicoccus sp. nov. isolated from the stool of a 2-year-old Nigerian boy with kwashiorkor. M. massiliensis is Gram positive, facultatively anaerobic, nonsporulating and motile. The 3 842 438 bp long genome contains 3362 protein-coding and 49 RNA genes, including one 5S rRNA gene, one 16S rRNA gene, one 23S rRNA gene and 46 tRNA genes.

Published
2016

305. Christensenella massiliensis, a new bacterial species isolated from the human gut

Author

Didier Raoult, S. Khelaifia, Pierre-Edouard Fournier, S. Ndongo, 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), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and INSB-INSB-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, biology, gut microbiota, 030106 microbiology, New Species, taxonogenomics, Stool specimen, Gut flora, culturomics, biology.organism_classification, Microbiology, lcsh:Infectious and parasitic diseases, 3. Good health, Christensenella massiliensis, 03 medical and health sciences, taxonomy, 030104 developmental biology, Infectious Diseases, Human gut, Culturomics, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lcsh:RC109-216, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; We describe the main characteristics of Christensenella massiliensis, strain Marseille-P2438(T) (CSUR P2438), isolated from a stool specimen of a 66-year-old patient.

Published
2016

306. Isolation of new species 'Peptoniphilus phoceensis' from human gut

Author

J. Rathored, Didier Raoult, M. Million, Si Traore, Caroline Michelle, Gaël Mourembou, J.-C. Lagier, Saber Khelaifia, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), 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), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Culturomics, biology, Stool sample, gut microbiota, 030106 microbiology, New Species, taxonogenomics, Gut flora, biology.organism_classification, Isolation (microbiology), Microbiology, Peptoniphilus phoceensis, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Infectious Diseases, Human gut, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, “Peptoniphilus phoceensis” sp. nov, lcsh:RC109-216, human, Bacteria, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; Taxonogenomics coupled with culturomics leads to descriptions of new bacteria. Thanks to this strategy, we report the main characteristics of "Peptoniphilus phoceensis" strain SIT15, a new bacterium isolated from a stool sample of a 1-year-old healthy Senegalese boy.

Published
2016

307. Non-contiguous finished genome sequence and description of Streptococcus varani sp. nov

Author

S, Bakour, J, Rathored, C I, Lo, O, Mediannikov, M, Beye, C B, Ehounoud, P, Biagini, D, Raoult, P-E, Fournier, and F, Fenollar

Subjects
Culturomics, taxonogenomics, Varanus niloticus, genome, Streptococcus varani, Taxonogenomics: Genome of a New Organism
Abstract

Strain FF10(T) (= CSUR P1489 = DSM 100884) was isolated from the oral cavity of a lizard (Varanus niloticus) in Dakar, Senegal. Here we used a polyphasic study including phenotypic and genomic analyses to describe the strain FF10(T). Results support strain FF10(T) being a Gram-positive coccus, facultative anaerobic bacterium, catalase-negative, non-motile and non-spore forming. The sequenced genome counts 2.46 Mb with one chromosome but no plasmid. It exhibits a G+C content of 40.4% and contains 2471 protein-coding and 45 RNA genes. On the basis of these data, we propose the creation of Streptococcus varani sp. nov.

Published
2016

308. ‘Mediterranea massiliensis’ gen. nov., sp. nov., a new human-associated bacterium isolated from the right and left colon lavage of a 58-year-old patient

Author

Didier Raoult, Saber Khelaifia, Pierre-Edouard Fournier, M. Mailhe, D. Ricaboni, A. Benezech, 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), Clinic of Infectious Diseases, Luigi Sacco Hospital, Università degli Studi di Milano = University of Milan (UNIMI), INSB-INSB-Centre National de la Recherche Scientifique (CNRS), and University of Milan

Subjects
0301 basic medicine, Culturomics, biology, education, Mediterranea massiliensis, taxonogenomics, biology.organism_classification, Microbiology, 3. Good health, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, taxonomy, 030104 developmental biology, Infectious Diseases, Left colon, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, genomics, Taxonomy (biology), lcsh:RC109-216, Bacteria, ComputingMilieux_MISCELLANEOUS, health care economics and organizations
Abstract

International audience; We report here the main characteristics of 'Mediterranea massiliensis' strain Marseille-P2645(T) (CSURP2645) that was isolated from stored samples of gut.

Published
2016

309. Noncontiguous finished genome sequence and description of Bacillus testis strain SIT10 sp. nov

Author

T. Cimmino, Cheikh Sokhna, Didier Raoult, Jean-Marc Rolain, S. Le Page, Aldiouma Diallo, S.I. Traore, C. Valentini, 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, 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), 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, 030106 microbiology, Bacillus testis, taxonogenomics, Microbiology, Genome, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, 23S ribosomal RNA, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lcsh:RC109-216, Gene, ComputingMilieux_MISCELLANEOUS, Genetics, Whole genome sequencing, Bacillaceae, biology, culturomics, 16S ribosomal RNA, biology.organism_classification, 6. Clean water, 030104 developmental biology, Infectious Diseases, Culturomics, GC-content, Taxonogenomics: Genome of a New Organism
Abstract

International audience; Bacillus testis strain SIT10 (= CSUR P1492=DSMZ 101190) is the new type strain collected from stool from a 2-year-old boy from Senegal during a culturomics study. This Gram-positive bacterium is a facultative anaerobic rod and a member of the Bacillaceae family. We describe here the features of this bacterium, together with the complete genome sequence and annotation. The 3987349bp long genome (one chromosome but no plasmid) with 42.8% GC content contains 4005 protein-coding and 171 sRNA genes, including 19 5S rRNA gene, 15 16S rRNA genes and ten 23S rRNA genes.

Published
2016

310. Microvirga massiliensis sp nov., the human commensal with the largest genome

Author

Caputo, Aurelia, Lagier, Jean-Christophe, Azza, Said, Robert, Catherine, Mouelhi, Donia, Fournier, Pierre-Edouard, Raoult, Didier, Assistance Publique - Hôpitaux de Marseille (APHM), 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
Male, Microvirga massiliensis, Culturomics, Adolescent, Computational Biology, large genome, Molecular Sequence Annotation, Genomics, Sequence Analysis, DNA, taxonogenomics, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Bacterial Typing Techniques, Gastrointestinal Microbiome, Phenotype, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Humans, Metagenome, France, Metagenomics, Genome, Bacterial, Phylogeny, Original Research, Alphaproteobacteria
Abstract

International audience; Microvirga massiliensis sp. nov. strain JC119(T) is a bacteria isolated in Marseille from a stool sample collected in Senegal. The 16S rRNA (JF824802) of M.massiliensis JC119(T) revealed 95% sequence identity with Microvirga lotononidis WSM3557(T) (HM362432). This bacterium is aerobic, gram negative, catalase positive, and oxidase negative. The draft genome of M.massiliensis JC119(T) comprises a 9,207,211-bp-long genome that is the largest bacterial genome of an isolate in humans. The genome exhibits a G+C content of 63.28% and contains 8685 protein-coding genes and 77 RNA genes, including 21 rRNA genes. Here, we describe the features of M.massiliensis JC119(T), together with the genome sequence information and its annotation.

Published
2016

311. Anaeromassilibacillus senegalensis gen. nov., sp. nov., isolated from the gut of a child with kwashiorkor

Author

Didier Raoult, Aldiouma Diallo, E. Guilhot, Saber Khelaifia, M. Tidjani Alou, 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 Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Anaeromassilibacillus senegalensis, 030106 microbiology, New Species, Kwashiorkor, taxonogenomics, Biology, culturomics, medicine.disease, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, taxonomy, 030104 developmental biology, Infectious Diseases, Culturomics, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, medicine, genomics, Taxonomy (biology), lcsh:RC109-216, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; We report the main characteristics of Anaeromassilibacillus senegalensis strain mt9(T) (= CSUR P1511) isolated from the stool of a 1-year-old kwashiorkor patient from Senegal.

Published
2016

312. Numidum massiliense gen. nov., sp. nov., a new member of the Bacillaceae family isolated from the human gut

Author

Nicholas Armstrong, M. Tidjani Alou, Didier Raoult, Pierre-Edouard Fournier, J. Rathored, T-T Nguyen, J.-C. Lagier, Saber Khelaifia, Assistance Publique - Hôpitaux de Marseille (APHM), 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 Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, 030106 microbiology, taxonogenomics, Microbiology, Genome, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Genus, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lcsh:RC109-216, Gene, Bacillaceae, ComputingMilieux_MISCELLANEOUS, Whole genome sequencing, Culturomics, biology, gut microbiota, Strain (biology), Ribosomal RNA, biology.organism_classification, 030104 developmental biology, Infectious Diseases, Numidum massiliense genome, Taxonogenomics: Genome of a New Organism
Abstract

International audience; Numidum massiliense gen. nov., sp. nov., strain mt3(T) is the type strain of Numidum gen. nov., a new genus within the family Bacillaceae. This strain was isolated from the faecal flora of a Tuareg boy from Algeria. We describe this Gram-positive facultative anaerobic rod and provide its complete annotated genome sequence according to the taxonogenomics concept. Its genome is 3755739bp long and contains 3453 protein-coding genes and 64 RNA genes, including eight rRNA genes.

Published
2016

313. Non-contiguous finished genome sequence and description of Streptococcus varani sp. nov

Author

Bakour, S., Rathored, J., Lo, C.I., Mediannikov, O., Beye, M., Ehounoud, C.B., Biagini, P., Raoult, D., Fournier, P.-E., Fenollar, F., 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, Emergence des Pathologies Virales (EPV), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), King Fahd Medical Research Center, Special Infectious Agents Unit, King Abdulaziz University, ANR-10-IAHU-0003,Méditerranée Infection,I.H.U. Méditerranée Infection(2010), INSB-INSB-Centre National de la Recherche Scientifique (CNRS), 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, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)

Subjects
Culturomics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], lcsh:RC109-216, taxonogenomics, Varanus niloticus, genome, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Streptococcus varani, lcsh:Infectious and parasitic diseases
Abstract

International audience; Strain FF10 T (= CSUR P1489 = DSM 100884) was isolated from the oral cavity of a lizard (Varanus niloticus) in Dakar, Senegal. Here we used a polyphasic study including phenotypic and genomic analyses to describe the strain FF10 T. Results support strain FF10 T being a Gram-positive coccus, facultative anaerobic bacterium, catalase-negative, non-motile and non-spore forming. The sequenced genome counts 2.46 Mb with one chromosome but no plasmid. It exhibits a G+C content of 40.4% and contains 2471 protein-coding and 45 RNA genes. On the basis of these data, we propose the creation of Streptococcus varani sp. nov.

Published
2016

314. 'Bariatricus massiliensis' as a new bacterial species from human gut microbiota

Author

Simon Bessis, Grégory Dubourg, Togo Amadou, Didier Raoult, 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, INSB-INSB-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)

Subjects
0303 health sciences, Culturomics, 030306 microbiology, business.industry, New Species, taxonogenomics, Bioinformatics, Microbiology, lcsh:Infectious and parasitic diseases, taxonomy, 03 medical and health sciences, “Bariatricus massiliensis”, Infectious Diseases, Human gut, Bariatricus massiliensis, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, genomics, Medicine, lcsh:RC109-216, business, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract

International audience; We report here the main phenotypic characteristics of "Bariatricus massiliensis" strain AT12 (CSUR P2179), isolated from the stool of a 58-year-old woman who underwent bariatric surgery.

Published
2016

315. Haloferax massiliensis sp. nov., the first human-associated halophilic archaea

Author

Saber Khelaifia, Didier Raoult, Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), 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), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Culturomics, biology, 030106 microbiology, New Species, Haloferax massiliensis, taxonogenomics, Stool specimen, biology.organism_classification, Microbiology, Halophile, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, taxonomy, 030104 developmental biology, Infectious Diseases, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Female patient, genomics, lcsh:RC109-216, ComputingMilieux_MISCELLANEOUS, Archaea
Abstract

International audience; We report the main characteristics of Haloferax massiliensis strain Arc-Hr(T) (= CSUR P974) isolated from stool specimen of a 22-year-old Amazonian obese female patient.

Published
2016

316. ‘Bacteroides ihuae’ sp. nov., a new bacterial species isolated from the human respiratory microbiome

Author

Maxime Descartes Mbogning Fonkou, Aurélie Morand, Pierre-Edouard Fournier, Grégory Dubourg, Didier Raoult, 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), and INSB-INSB-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, 030106 microbiology, New Species, taxonogenomics, Biology, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, taxonomy, medicine, genomics, lcsh:RC109-216, Microbiome, ‘Bacteroides ihuae’, food and beverages, culturomics, 3. Good health, Infectious Diseases, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Culturomics, Sputum, Taxonomy (biology), Bacteroides ihuae, medicine.symptom, 'Bacteroides ihuae'
Abstract

International audience; We present the main features of 'Bacteroides ihuae' sp. nov., strain Marseille-P2824(T) (CSUR P2824), isolated from the sputum of healthy Frenchwoman living in Marseille.

Published
2017
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317. ‘Tidjanibacter massiliensis’ gen. nov., sp. nov., a new bacterial species isolated from human colon

Author

Didier Raoult, M. Mailhe, Pierre-Edouard Fournier, D. Ricaboni, Jean-Christophe Lagier, A. Benezech, 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, 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, Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), Assistance Publique - Hôpitaux de Marseille (APHM), 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, and INSB-INSB-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, 030106 microbiology, ‘Tidjanibacter massiliensis’, taxonogenomics, Biology, Gut flora, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, medicine, lcsh:RC109-216, Irritable bowel syndrome, new species, Culturomics, gut microbiota, Strain (biology), Tidjanibacter massiliensis, medicine.disease, biology.organism_classification, digestive system diseases, 3. Good health, 'Tidjanibacter massiliensis', [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Infectious Diseases, Human colon
Abstract

International audience; We report the summary of main characteristics of Tidjanibacter massiliensis strain Marseille-P3084(T), a new bacterial species isolated from the liquid sample of the colon of a patient with a history of irritable bowel syndrome.

Published
2016

318. Vaginimicrobium propionicum gen. nov., sp. nov., a novel propionic acid bacterium derived from human vaginal discharge.

Author

Diop K, Cadoret F, Nguyen TT, Baudoin JP, Armstrong N, Raoult D, Bretelle F, Fournier PE, and Fenollar F

Subjects
Bacteria, Anaerobic isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids chemistry, Female, France, Humans, Propionates, Propionibacteriaceae isolation & purification, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Bacteria, Anaerobic classification, Phylogeny, Propionibacteriaceae classification, Vaginal Discharge microbiology
Abstract

A Gram-stain-positive anaerobic rod-shaped bacterium, designated strain Marseille-P3275 T , was isolated using culturomics from the vaginal discharge of healthy French woman. Marseille-P3275 T was non-motile and did not form spores. Cells had neither catalase nor oxidase activity. The major fatty acids were C 16 : 0 (29 %), C 18:1 ω9 (18 %), and iso-C 15 : 0 (17 %). The genomic DNA G+C content was 50.64 mol%. The phylogenetic analysis based on 16S rRNA gene sequence indicated that Marseille-P3275 T was related to members of the family Propionibacteriaceae (between 90.32-92.92 % sequence similarity) with formation of a clade with the monospecific genus Propionimicrobium (type species Propionimicrobium lymphophilum ). On the basis of these phylogenetic and phenotypic differences, Marseille-P3275 T was classified in a novel genus, Vaginimicrobium , as Vaginimicrobium propionicum gen. nov., sp. nov. The type strain is Marseille-P3275 T (=CSUR P3275 T =CECT 9677 T ).

Published
2020
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319. Gorillibacterium timonense sp. nov., isolated from an obese patient.

Author

Ndongo S, Beye M, Labas N, Di Pinto F, Richez M, Lagier JC, Fournier PE, Raoult D, and Bittar F

Subjects
Bacillales genetics, Bacillales isolation & purification, Base Composition, DNA, Bacterial genetics, Fatty Acids analysis, Feces microbiology, Genomics, Humans, Obesity, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Species Specificity, Bacillales classification, Phylogeny
Abstract

A Gram-negative and facultative anaerobic bacterium, designated strain SN4 T , was isolated from the stool sample of an obese Amazonian patient. The new isolate was characterized by the taxonogenomics approach. The strain SN4 T was beige-colored, circular and not haemolytic. Cells are rod shaped and motile with several flagella. Strain SN4 T grows optimally at pH 7 and can survive in the presence of a saline concentration of up to 75 g/l NaCl. The 16S ribosomal RNA gene sequence analysis of the novel strain SN4 T showed 95.28% similarity in nucleotide sequence with Gorillibacterium massiliense G5 T , the phylogenetically closest neighbor and the type species of this genus. Anteiso-C 15:0 , iso-C 15:0 and C 16:0 were found as the major components in the cellular fatty acid analysis of this isolate. The genomic draft of strain SN4 T is 5,263,742 bp long with 53.33% of G+C content. The differences in physiological, biochemical characteristics and phylogenetic and genomic data make it possible to clearly distinguish the strain SN4 T from G. massiliense G5 T . Based on the taxonogenomic description and the phenotypic and biochemical characteristics of this bacterium presented in this article, we propose the SN4 T strain (= CSUR P2011 = DSM 100,698) as a new species, Gorillibacterium timonense sp. nov.

Published
2020
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320. Draft genome and description of Chryseobacterium phocaeense sp. nov.: a new bacterial species isolated from the sputum of a cystic fibrosis patient.

Author

Abou Abdallah R, Okdah L, Bou Khalil J, Anani H, Fournier PE, Raoult D, and Bittar F

Subjects
Adolescent, Base Composition, Chryseobacterium chemistry, DNA, Bacterial genetics, Fatty Acids analysis, Female, Genome, Bacterial genetics, Humans, Nucleic Acid Hybridization, RNA, Ribosomal, 16S genetics, Sequence Homology, Nucleic Acid, Species Specificity, Sputum microbiology, Chryseobacterium classification, Chryseobacterium genetics, Cystic Fibrosis microbiology, Phylogeny
Abstract

Strain 6021061333 T was isolated from the sputum of 16-year-old girl with cystic fibrosis following a pulmonary exacerbation. This bacterial strain could not be identified by our systematic MALDI-TOF mass spectrometry screening on a MicroFlex. This led to the sequencing of the 16S rRNA gene, which shows 97.83% sequence identity with Chryseobacterium kwangjuense strain KJ1R5 T , the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. Colonies are yellow, circular and 0.5-1 mm in diameter after cultivation at 28 °C for 24 h on 5% sheep blood-enriched Colombia agar. Growth occurs at temperatures in the range of 28-37 °C (optimally at 28 °C). Strain 6021061333 T is Gram-negative, non-motile and strictly aerobic bacillus. It is catalase and oxidase positive. The 4,864,678 bp-long genome, composed of five contigs, has a G+C content of 38.86%. Out of the 4427 predicted genes, 4342 were protein-coding genes and 85 were RNAs. The major fatty acids are branched (13-methyl-tetradecanoic acid and 15-methyl-hexadecenoic acid). Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity (ANI) of the strain 6021061333 T against genomes of the type strains of related species ranged between 23.60 and 50.40% and between 79.31 and 93.06%, respectively. According to our taxonogenomics results, we propose the creation of Chryseobacterium phocaeense sp. nov. that contains the type strain 6021061333 T (= CSUR P2660, = CECT 9670).

Published
2019
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321. ‘Clostridium mediterraneense,’ a new bacterial species isolated from the human gut.

Author

Ndongo, S., Cassir, N., Delerce, J., Raoult, D., and La Scola, B.

Subjects
*CLOSTRIDIUM diseases, *CLOSTRIDIUM disease treatment, *CLOSTRIDIUM biotechnology, *PEOPLE with diabetes, *DIAGNOSIS, *MEDICAL care
Abstract

We report the main characteristics of ‘Clostridium mediterraneense’ sp. nov., strain Marseille-P2434 T (CSUR P2434), a new species within the genus Clostridium. This strain was isolated from the gut microbiota of a 66-year-old diabetic patient in Marseille, France. [ABSTRACT FROM AUTHOR]

Published
2017
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322. ‘Bacteroides ihuae’ sp. nov., a new bacterial species isolated from the human respiratory microbiome.

Author

Fonkou, M.D.M., Morand, A., Fournier, P.-E., Raoult, D., and Dubourg, G.

Subjects
*BACTEROIDES, *BACTERIA classification, *SPUTUM microbiology, *BACTERIAL cultures, *FRENCH people, *DISEASES
Abstract

We present the main features of ‘Bacteroides ihuae’ sp. nov., strain Marseille-P2824 T (CSUR P2824), isolated from the sputum of healthy Frenchwoman living in Marseille. [ABSTRACT FROM AUTHOR]

Published
2017
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323. ‘Traorella massiliensis’ gen. nov., sp. nov., a new bacterial species isolated from the left colon of a 76-year-old woman.

Author

Mailhe, M., Ricaboni, D., Vitton, V., Lagier, J.-C., Fournier, P.-E., and Raoult, D.

Subjects
*COLON microbiology, *BACTERIA classification, *DISEASES in older women, *BACTERIAL cultures, *BACTERIAL genomes
Abstract

We present here the summary of main characteristics of ‘Traorella massiliensis’ strain Marseille-P3110 T , which was isolated from a left colon liquid sample of a 76-year-old woman. [ABSTRACT FROM AUTHOR]

Published
2017
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324. ‘Tidjanibacter massiliensis’ gen. nov., sp. nov., a new bacterial species isolated from human colon.

Author

Mailhe, M., Ricaboni, D., Benezech, A., Lagier, J.-C., Fournier, P.-E., and Raoult, D.

Subjects
*BACTERIA classification, *COLON microbiology, *IRRITABLE colon, *HISTORY of medicine, *GUT microbiome
Abstract

We report the summary of main characteristics of Tidjanibacter massiliensis strain Marseille-P3084 T , a new bacterial species isolated from the liquid sample of the colon of a patient with a history of irritable bowel syndrome. [ABSTRACT FROM AUTHOR]

Published
2017
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325. ‘Ileibacterium massiliense’ gen. nov., sp. nov., a new bacterial species isolated from human ileum of a patient with Crohn disease.

Author

Mailhe, M., Ricaboni, D., Vitton, V., Lagier, J.-C., Fournier, P.-E., and Raoult, D.

Subjects
*BACTERIA classification, *CROHN'S disease, *ILEUM diseases, *BACTERIAL cultures, *GUT microbiome
Abstract

We propose here the main characteristics of ‘Ileibacterium massiliense’ strain Marseille-P3115, which was isolated from the ileum liquid sample of a patient with Crohn disease. [ABSTRACT FROM AUTHOR]

Published
2017
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326. ‘Colibacter massiliensis’ gen. nov., sp. nov., a new bacterial species isolated from human left colon.

Author

Mailhe, M., Ricaboni, D., Vitton, V., Cadoret, F., Fournier, P.-E., and Raoult, D.

Subjects
*COLON microbiology, *BACTERIAL cultures, *OLDER men, *BACTERIA classification, *GUT microbiome, *DISEASES in older people
Abstract

We present here the main characteristics of the strain Marseille-P2911 (= CSUR P2911 = DSMZ 103304), a bacterial species isolated from the left colon liquid sample of a 60-year-old man. [ABSTRACT FROM AUTHOR]

Published
2017
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327. “Intestinimonas massiliensis” sp. nov, a new bacterium isolated from human gut.

Author

Durand, G., Afouda, P., Raoult, D., and Dubourg, G.

Subjects
*BACTERIA, *GENOMICS, *ENTEROTYPES, *RIBOSOMAL RNA, *SPECTROMETERS
Abstract

Here we report the main features of the proposed new bacterial species “ Intestinimonas massiliensis ” sp. nov. The type strain GD2 T (CSUR = P1930) was isolated from the gut microbiota of a healthy patient using a culturomics approach combined with taxonogenomics. [ABSTRACT FROM AUTHOR]

Published
2017
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328. 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

Yimagou, E.K., Anani, H., Yacouba, A., Hasni, I., Baudoin, J.-P., Raoult, D., and Bou Khalil, J.Y.

Subjects
*DENTAL care, *URINE, *BACTERIA
Abstract

Urinicoccus massiliensis strain Marseille-P1992T (= CSURP1992 = DSM100581) is a species of a new genus isolated from human urine. [ABSTRACT FROM AUTHOR]

Published
2019
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330. Brachybacterium massiliense sp. nov., a new bacterium isolated from stool from a healthy Senegalese child.

Author

Mekhalif, F., Tidjani Alou, M., Zgheib, R., Lo, C.I., Fournier, P.-E., Raoult, D., and Lagier, J.-C.

Subjects
*RNA sequencing, *RIBOSOMAL RNA, *SENEGALESE
Abstract

Based on our phenotypic and genotypic analyses, Brachybacterium massiliense strain Marseille-P2240T (= CSURP2240; = DSM 101766) is a new species isolated from stool of a healthy subject. The strain was stained Gram-positive. It was aerobic, catalase-positive and oxidase-negative. Its optimal growth occurs at 37°C in aerobic condition. The 16S ribosomal RNA sequence analysis revealed that strain Marseille-P2240T shown 98.18% similarity with Brachybacterium saurashtrense strain JG 06, the more closely related species with standing in nomenclature. [ABSTRACT FROM AUTHOR]

Published
2019
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331. Corynebacterium senegalense sp. nov. and Arthrobacter senegalensis sp. nov., two new Actinobacteria isolated from skin swab from the palm of hand.

Author

Ndiaye, C., Fall, N.S., Kuete, E., Lo, C.I., Raoult, D., Sokhna, C., and Lagier, J.-C.

Subjects
*CORYNEBACTERIUM, *ARTHROBACTER, *ACTINOBACTERIA, *SKIN, *PALMS
Abstract

Corynebacterium senegalense strain Marseille-P4329T (= CSURP4329) and Arthrobacter senegalensis strain Marseille-P4329T (= CSURP4198) are new species first isolated from human skin. A culturomics approach and taxonogenomics methods were used for these new bacterial species. [ABSTRACT FROM AUTHOR]

Published
2019
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333. Genome sequence and description of Bacteroides bouchesdurhonensis sp. nov., a new anaerobic bacterium isolated from the human gut.

Author

Ndongo, S., Tall, M.L., Ngom, I.I., Fournier, P.-E., Levasseur, A., Raoult, D., and Khelaifia, S.

Subjects
*ANAEROBIC bacteria, *BACTEROIDES, *NUCLEOTIDE sequencing, *BACTEROIDES fragilis, *HUMAN microbiota, *GUT microbiome
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. [ABSTRACT FROM AUTHOR]

Published
2019
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334. Genome sequence and description of Coprococcus phoceensis gen. nov., sp. nov., a new bacterial genus isolated from the human left colon.

Author

Bonnet, M., Ricaboni, D., Mailhe, M., Vitton, V., Benezech, A., Delerce, J., Raoult, D., Cassir, N., Lascola, B., and Khelaifia, S.

Subjects
*MASS spectrometry, *TIME-of-flight mass spectrometry, *CROHN'S disease, *NUCLEOTIDE sequencing, *GUT microbiome
Abstract

We report here the main characteristics of Coprococcus phoceensis strain Marseille-P3062T (CSUR P3062). The 16S rDNA sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry spectrum analysis were used to identify and characterize this new anaerobic bacterial species, which was isolated from the left colon cleansing of a 25-year-old French man with Crohn's disease. [ABSTRACT FROM AUTHOR]

Published
2019
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335. Virgibacillusndiopensis sp. nov., a new halophilic bacterium isolated from the stool of a healthy 11-year-old boy.

Author

Francis, R., Anani, H., Fontanini, A., Fournier, P.E., Scola, B.L.A., Raoult, D., and Bou Khalil, J.Y.

Subjects
*HALOBACTERIUM, *HALOMONAS (Bacteria), *GOLD, *BOYS
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. [ABSTRACT FROM AUTHOR]

Published
2019
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336. Genome sequence and description of Traorella massiliensis gen. nov., sp. nov., a new bacterial genus isolated from human left colon.

Author

Bonnet, M., Mailhe, M., Ricaboni, D., Labas, N., Richez, M., Vitton, V., Benezech, A., Fournier, P.-E., Million, M., Raoult, D., and Khelaifia, S.

Subjects
*NUCLEOTIDE sequencing, *GRAM-negative anaerobic bacteria, *RIBOSOMAL RNA, *GENOMES
Abstract

A strictly anaerobic, motile, non–spore-forming, Gram-negative, rod-shaped bacterium designated Marseille-P3110T was isolated from the left colon cleansing of a 76-year-old Frenchwoman. Its 16S ribosomal RNA (rRNA) gene showed a 93.2% similarity level with the 16S rRNA of Dielma fastidiosa strain JC13, the closest species with a validly published name. The genome of Marseille-P3110T is 2 607 061 bp long with 35.99% G+C content. Of the 2642 predicted genes, 2582 were protein-coding genes and 60 were RNAs, including five 16S rRNA genes. [ABSTRACT FROM AUTHOR]

Published
2019
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337. Anaerotruncus massiliensis sp. nov., a succinate-producing bacterium isolated from human stool from an obese patient after bariatric surgery.

Author

Togo, A.H., Diop, A., Dubourg, G., Khelaifia, S., Richez, M., Armstrong, N., Maraninchi, M., Fournier, P.-E., Raoult, D., and Million, M.

Subjects
*BARIATRIC surgery, *NUCLEOTIDE sequence, *RIBOSOMAL RNA, *GRAM-negative aerobic bacteria, *BACTERIA, *GUT microbiome
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. [ABSTRACT FROM AUTHOR]

Published
2019
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338. Genome sequence and description of Pantoea septica strain FF5

Author

Florence Fenollar, Cheikh Ibrahima Lo, Didier Raoult, Thi Tien Nguyen, Pierre-Edouard Fournier, Oleg Mediannikov, and Roshan Padhmanabhan

Subjects
Whole genome sequencing, Genetics, Genome, Culturomics, Taxonogenomics, Strain (chemistry), Pantoea septica, Biology, rpoB, Senegal, Short Genome Report, Plasmid, RRNA Operon, Gene
Abstract

Strain FF5 was isolated from the skin flora of a healthy Senegalese 35-year-old woman. This strain was identified as belonging to the species Pantoea septica based on rpoB sequence identity of 99.7 % with Pantoea septica strain LMG 5345T and a highest MALDI-TOF-MS score of 2.3 with Pantoea septica. Like P. septica, this FF5 strain is a Gram-negative, aerobic, motile, and rod-shaped bacterium. Currently, 17 genomes have been sequenced within the genus Pantoea but none for Pantoea septica. Herein, we compared the genomic properties of strain FF5 to those of other species within the genus Pantoea. The genome of this strain is 4,548,444 bp in length (1 chromosome, no plasmid) with a G + C content of 59.1 % containing 4125 protein-coding and 68 RNA genes (including 2 rRNA operons). We also performed an extensive phenotypic analysis showing new phenotypic characteristics such as the production of alkaline phosphatase, acid phosphatase and naphthol-AS-BI-phosphohydrolase. Electronic supplementary material The online version of this article (doi:10.1186/s40793-015-0083-0) contains supplementary material, which is available to authorized users.

Published
2015

339. Genome sequence and description of Mannheimia massilioguelmaensis sp. nov

Author

Hadjadj, L., Bentorki, Ahmed Aimen, Michelle, C., Amoura, K., Djahoudi, Abdelghani, Rolain, Jean-Marc, 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), Laboratoire de microbiologie, CHU Dorban, Université Badji Mokhtar - Annaba [Annaba] (UBMA), Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS), and Université Badji Mokhtar Annaba (UBMA)

Subjects
Genome, Mannheimia massilioguelmaensis, infectious disease, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], lcsh:RC109-216, human infection, taxonogenomics, [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; Strain MG13 T sp. nov. is the type strain of Mannheimia massilioguelmaensis, a new species within the genus Mannheimia. This strain was isolated from the exudate of a skin lesion of an Algerian man. Mannheimia massilioguelmaensis is a Gram-negative, facultative anaerobic rod, member of the family Pasteurellaceae. Here we describe this organism, together with the complete genome sequence and annotation. The 2 186 813 bp long genome contains 2048 protein-coding and 55 RNA genes, including eight rRNA genes.

Published
2015

340. Genome sequence and description of Anaerosalibacter massiliensis sp. nov

Author

Pierre-Edouard Fournier, Didier Raoult, C. Michele, Magali Richez, Jônatas Santos Abrahão, S.A. Sankar, Nicholas Armstrong, J.-C. Lagier, Saber Khelaifia, and Niokhor Dione

Subjects
0301 basic medicine, 030106 microbiology, Clostridiaceae, taxonogenomics, Biology, Microbiology, Genome, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Plasmid, lcsh:RC109-216, Gene, genome, Whole genome sequencing, Genetics, Chromosome, Ribosomal RNA, culturomics, biology.organism_classification, 030104 developmental biology, Infectious Diseases, Culturomics, Anaerosalibacter massiliensis, Taxonogenomics: Genome of a New Organism
Abstract

Anaerosalibacter massiliensis sp. nov. strain ND1T (= CSUR P762 = DSM 27308) is the type strain of A. massiliensis sp. nov., a new species within the genus Anaerosalibacter. This strain, the genome of which is described here, was isolated from the faecal flora of a 49-year-old healthy Brazilian man. Anaerosalibacter massiliensis is a Gram-positive, obligate anaerobic rod and member of the family Clostridiaceae. With the complete genome sequence and annotation, we describe here the features of this organism. The 3 197 911 bp long genome (one chromosome but no plasmid) contains 3271 protein-coding and 62 RNA genes, including six rRNA genes.

Published
2015

341. Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut

Author

F. Di Pinto, Saber Khelaifia, J. Rathored, Cheikh Sokhna, Catherine Robert, Olivier Croce, J.-C. Lagier, Carine Couderc, Didier Raoult, and El hadji Seck

Subjects
moderately halophilic bacteria, Culturomics, biology, Strain (chemistry), taxonogenomics, Flagellum, biology.organism_classification, Microbiology, Genome, Halophile, lcsh:Infectious and parasitic diseases, Infectious Diseases, Plasmid, Virgibacillus senegalensis, lcsh:RC109-216, Taxonogenomics: Genome of a new organism, Gene, genome, Bacteria, human gut
Abstract

Virgibacillus senegalensis SK-1T (= CSUR P1101 = DSM 28585) is the type strain of V. senegalensis sp. nov. It is an aerobic, Gram positive, moderately halophilic, motile bipolar flagellum isolated from a healthy Senegalese man. Here we describe the genomic and phenotypic characteristics of this isolate. The 3 755 098 bp long genome (one chromosome, no plasmid) exhibits a G + C content of 42.9% and contains 3738 protein-coding and 95 RNA genes.

Published
2015

342. Noncontiguous finished genome sequence and description of Paenibacillus antibioticophila sp. nov. GD11(T), the type strain of Paenibacillus antibioticophila

Author

Jean-Marc Rolain, T. Cimmino, Didier Raoult, P. Brouqui, P.-E. Fournier, Catherine Robert, S.a. Senkar, J.-C. Lagier, Christophe Flaudrops, and Grégory Dubourg

Subjects
Genetics, Whole genome sequencing, Paenibacillus antibioticophila, Culturomics, biology, Strain (biology), RNA, taxonogenomics, biology.organism_classification, Microbiology, Genome, lcsh:Infectious and parasitic diseases, Infectious Diseases, Type (biology), New Microbes in Humans, lcsh:RC109-216, Gene, genome, Bacteria
Abstract

Paenibacillus antibioticophila strain GD11T sp. nov. is the type strain of a new species within the genus Paenibacillus. This strain, whose genome is described here, was isolated from human faeces of a 63-year-old woman with multidrug-resistant tuberculosis who was receiving numerous antibiotics at the time of stool collection. P. antibioticophila is a Gram-positive aerobic bacterium. We describe here the features of this bacterium, together with the complete genome sequence and annotation. The 5 562 631 bp long genome contains 5084 protein-coding and 71 RNA genes.

Published
2015

343. Genome sequence and description of Pantoea septica strain FF5

Author

Lo, C. I., Padhmanabhan, R., Mediannikov, Oleg, Nguyen, T. T., Raoult, Didier, Fournier, P. E., and Fenollar, F.

Subjects
Genome, Culturomics, Taxonogenomics, Pantoea septica, Senegal
Abstract

Strain FF5 was isolated from the skin flora of a healthy Senegalese 35-year-old woman. This strain was identified as belonging to the species Pantoea septica based on rpoB sequence identity of 99.7 % with Pantoea septica strain LMG 5345(T) and a highest MALDI-TOF-MS score of 2.3 with Pantoea septica. Like P. septica, this FF5 strain is a Gram-negative, aerobic, motile, and rod-shaped bacterium. Currently, 17 genomes have been sequenced within the genus Pantoea but none for Pantoea septica. Herein, we compared the genomic properties of strain FF5 to those of other species within the genus Pantoea. The genome of this strain is 4,548,444 bp in length (1 chromosome, no plasmid) with a G + C content of 59.1 % containing 4125 protein-coding and 68 RNA genes (including 2 rRNA operons). We also performed an extensive phenotypic analysis showing new phenotypic characteristics such as the production of alkaline phosphatase, acid phosphatase and naphthol-AS-BI-phosphohydrolase.

Published
2015

344. High quality draft genome sequence and description of Occidentia massiliensis gen. nov., sp. nov., a new member of the family Rickettsiaceae

Author

Didier Raoult, Lesley Bell-Sakyi, Roshan Padmanabhan, Pierre-Edouard Fournier, Oleg Mediannikov, and Thi-Thien Nguyen

Subjects
Occidentia massiliensis, Whole genome sequencing, Genetics, Genome, Orientia tsutsugamushi, Taxonogenomics, Soft tick, Bacillus, Biology, bacterial infections and mycoses, biology.organism_classification, Ornithodoros sonrai, Orientia, Senegal, Short Genome Report, Type species, Genus, RRNA Operon
Abstract

The family Rickettsiaceae currently includes two genera: Orientia that contains one species, Orientia tsutsugamushi, and Rickettsia that contains 28 species. Occidentia massiliensis gen. nov., sp. nov. strain OS118(T) is the type strain of O. massiliensis gen. nov., sp. nov., the type species of the new genus Occidentia gen. nov. within the family Rickettsiaceae. This strain, whose genome is described here, was isolated in France from the soft tick Ornithodoros sonrai collected in Senegal. O. massiliensis is an aerobic, rod-shaped, Gram-negative, obligate intracellular bacillus that may be cultivated in BME/CTVM2 cells. Here we describe the features of O. massiliensis, together with the complete genomic sequencing and annotation. The 1,469,252 bp long genome (1 chromosome but no plasmid) contains 1,670 protein-coding and 41 RNA genes, including one rRNA operon.

Published
2014

345. ‘Colibacter massiliensis’ gen. nov., sp. nov., a new bacterial species isolated from human left colon

Author

M. Mailhe, Didier Raoult, Véronique Vitton, Frédéric Cadoret, D. Ricaboni, Pierre-Edouard Fournier, 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
0301 basic medicine, gut microbiota, Strain (biology), 030106 microbiology, New Species, ‘Colibacter massiliensis’, Colibacter massiliensis, 'Colibacter massiliensis', taxonogenomics, Biology, Gut flora, culturomics, biology.organism_classification, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, 030104 developmental biology, Infectious Diseases, Left colon, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Culturomics, microbiota, lcsh:RC109-216
Abstract

International audience; We present here the main characteristics of the strain Marseille-P2911 (= CSUR P2911 = DSMZ 103304), a bacterial species isolated from the left colon liquid sample of a 60-year-old man.

Published
2016

346. 'Lachnoclostridium bouchesdurhonense,' a new bacterial species isolated from human gut microbiota

Author

N. Cassir, B. La Scola, Michel Hosny, and T. Amadou

Subjects
0301 basic medicine, 030106 microbiology, New Species, taxonogenomics, Gut flora, Bioinformatics, Microbiology, digestive system, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Human gut, Medicine, lcsh:RC109-216, Lachnoclostridium, Culturomics, biology, gut microbiota, obese, business.industry, Strain (biology), biology.organism_classification, Infectious Diseases, “Lachnoclostridium bouchesdurhonense”, business
Abstract

We report the main characteristics of “Lachnoclostridium bouchesdurhonense” strain AT5T (=CSUR P2181), a new bacterial species isolated from the gut microbiota of an obese patient from Marseille.

Published
2016

347. Romboutsia timonensis, a new species isolated from human gut

Author

M. Million, D. Ricaboni, Didier Raoult, M. Mailhe, 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), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), and Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Romboutsia timonensis sp. nov, New Species, education, 030106 microbiology, Romboutsia timonensis, taxonogenomics, Biology, Microbiology, lcsh:Infectious and parasitic diseases, 03 medical and health sciences, Human gut, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, lcsh:RC109-216, human, ComputingMilieux_MISCELLANEOUS, Culturomics, Strain (biology), Human microbiome, 3. Good health, 030104 developmental biology, Infectious Diseases, gut, Human colon, Severe anaemia
Abstract

International audience; The exploration of the human microbiome was recently revolutionized by microbial culturomics and taxonogenomics. Thanks to this approach, we report here the main characteristics of Romboutsia timonensis strain Marseille-P326, a new bacterium isolated from the right human colon by colonoscopy in a 63-year-old French man with severe anaemia with melaena.

Published
2016

348. Bacillus kwashiorkori sp. nov., a new bacterial species isolated from a malnourished child using culturomics

Author

Saber Khelaifia, Caroline Michelle, Didier Raoult, Souleymane Brah, Fadi Bittar, Pierre-Edouard Fournier, Mamadou Beye, Sory Ibrahima Traore, Carine Couderc, El hadji Seck, 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 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 Biomédicale des Armées (IRBA)-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), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), and Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)

Subjects
DNA, Bacterial, 0301 basic medicine, 030106 microbiology, Bacillus, taxonogenomics, DNA, Ribosomal, Microbiology, Genome, Feces, 03 medical and health sciences, Cytosol, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, RNA, Ribosomal, 16S, Cluster Analysis, Humans, Bacillus kwashiorkori, genome, Gene, Phylogeny, Original Research, 2. Zero hunger, Genetics, Base Composition, biology, Strain (chemistry), Fatty Acids, Malnutrition, Temperature, Infant, Nucleic Acid Hybridization, Sequence Analysis, DNA, culturomics, biology.organism_classification, 16S ribosomal RNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Aerobiosis, Bacterial Typing Techniques, Type species, 030104 developmental biology, Culturomics, Genome, Bacterial, Locomotion, Orthologous Gene
Abstract

International audience; Strain SIT6(T) was isolated from the fecal flora of a severely malnourished child as part of a broad culturomics study aiming to maximize the culture conditions for the in-depth exploration of the human microbiota. An analysis of the 16S rRNA gene sequence showed that strain SIT6(T) shared 94.1% 16S rRNA gene sequence similarity with Bacillus thermoamylovorans DKPT (NR\₀29151), the phylogenetically closest type species. Colonies are creamy white, circular, 4-5 mm in diameter after cultivation at 37 degrees C for 24 hr on 5% sheep blood-enriched Colombia agar. Growth occurs at temperatures in the range of 25-56 degrees C (optimally at 37 degrees C). Strain SIT6(T) is a gram-positive, facultative anaerobic rod and motile by means of peritrichous flagella and sporulating; it is catalase and oxidase positive. The 2,784,637-bp-long genome, composed of 16 contigs, has a G+C content of 35.19%. Of the 2,646 predicted genes, 2,572 were protein-coding genes and 74 were RNAs. The major fatty acids are saturated species (15:0 iso, 16:0 and 17:0 anteiso). Of the 14 detected fatty acids, 11 are saturated, either linear or branched (iso and anteiso). Digital DNA-DNA hybridization (dDDH) estimation and average genomic identity of orthologous gene sequences (AGIOS) of the strain SIT6(T) against genomes of the type strains of related species ranged between 18.6% and 38.3% and between 54.77% and 65.50%, respectively. According to our taxonogenomics results, we propose the creation of Bacillus kwashiorkori sp. nov. that contains the type strain SIT6(T) (=CSUR P2452(T), =DSM 29059(T)).

Published
2017

349. Non-contiguous finished genome sequence and description of Bacillus massilioanorexius sp. nov

Author

Jean-Christophe Lagier, Catherine Robert, Didier Raoult, Pierre-Edouard Fournier, Ajay Kumar Mishra, and Anne Pfleiderer

Subjects
Genetics, Whole genome sequencing, Strain (biology), Chromosome, taxonogenomics, Biology, Ribosomal RNA, culturomics, Genome, Short Genome Reports, Plasmid, Culturomics, Bacillus massilioanorexius, Gene, genome
Abstract

Bacillus massilioanorexius strain AP8(T) sp. nov. is the type strain of B. massilioanorexius sp. nov., a new species within the genus Bacillus. This strain, whose genome is described here, was isolated from the fecal flora of a 21-year-old Caucasian French female suffering from a severe form of anorexia nervosa since the age of 12 years. B. massilioanorexius is a Gram-positive aerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,616,135 bp long genome (one chromosome but no plasmid) contains 4,432 protein-coding and 87 RNA genes, including 8 rRNA genes.

Published
2014

350. Non-contiguous finished genome sequence and description of Megasphaera massiliensis sp. nov

Author

Nicole Prisca Makaya Dangui, Pierre-Edouard Fournier, Jean-Christophe Lagier, Roshan Padmanabhan, Didier Raoult, Carine Couderc, and Caroline Michelle

Subjects
Whole genome sequencing, Genetics, animal structures, Chromosome, taxonogenomics, Biology, Ribosomal RNA, culturomics, biology.organism_classification, Genome, Short Genome Reports, Megasphaera massiliensis, Plasmid, Culturomics, Coccobacillus, Gene, genome
Abstract

Megasphaera massiliensis strain NP3(T) sp. nov. is the type strain of Megasphaera massiliensis sp. nov., a new species within the genus Megasphaera. This strain, whose genome is described here, was isolated from the fecal flora of an HIV-infected patient. M. massiliensis is a Gram-negative, obligate anaerobic coccobacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,661,757 bp long genome (1 chromosome but no plasmid) contains 2,577 protein-coding and 61 RNA genes, including 5 rRNA genes.

Published
2014

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