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Robert C, Cascella F, Mellai M, Barizzone N, Mignone F, Massa N, Nobile V, Bona E. Influence of Sex on the Microbiota of the Human Face. Microorganisms 2022; 10:microorganisms10122470. [PMID: 36557723 PMCID: PMC9786802 DOI: 10.3390/microorganisms10122470] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/24/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
The role of the microbiota in health and disease has long been recognized and, so far, the cutaneous microbiota in humans has been widely investigated. The research regarded mainly the microbiota variations between body districts and disease skin states (i.e., atopic dermatitis, psoriasis, acne). In fact, relatively little information is available about the composition of the healthy skin microbiota. The cosmetic industry is especially interested in developing products that maintain and/or improve a healthy skin microbiota. Therefore, in the present work, the authors chose to investigate in detail the structure and composition of the basal bacterial community of the face. Ninety-six cheek samples (48 women and 48 men) were collected in the same season and the same location in central northern Italy. Bacterial DNA was extracted, the 16S rDNA gene was amplified by PCR, the obtained amplicons were subjected to next generation sequencing. The principal members of the community were identified at the genus level, and statistical analyses showed significant variations between the two sexes. This study identified abundant members of the facial skin microbiota that were rarely reported before in the literature and demonstrated the differences between male and female microbiota in terms of both community structure and composition.
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Affiliation(s)
- Clémence Robert
- R&D Department, Complife Italia c/a Centre for Autoimmune and Allergic Diseases (CAAD), 22100 Novara, Italy
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
- Correspondence: (C.R.); (E.B.)
| | - Federica Cascella
- R&D Department, Complife Italia c/a Centre for Autoimmune and Allergic Diseases (CAAD), 22100 Novara, Italy
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
| | - Marta Mellai
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy
| | - Nadia Barizzone
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy
| | - Flavio Mignone
- Department of Science and Technologic Innovation, University of Eastern Piedmont, 15121 Alessandria, Italy
- SmartSeq s.r.l., 28100 Novara, Italy
| | - Nadia Massa
- Department of Science and Technologic Innovation, University of Eastern Piedmont, 15121 Alessandria, Italy
| | - Vincenzo Nobile
- R&D Department, Complife Italia c/a Centre for Autoimmune and Allergic Diseases (CAAD), 22100 Novara, Italy
| | - Elisa Bona
- Centre for Autoimmune and Allergic Diseases (CAAD), University of Eastern Piedmont, 28100 Novara, Italy
- Department for Sustainable Development and Ecological Transition, University of Eastern Piedmont, 13100 Vercelli, Italy
- Correspondence: (C.R.); (E.B.)
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Kim JH, Ko GP, Son KH, Ku BH, Bang MA, Kang MJ, Park HY. Arazyme in combination with dietary carbohydrolases influences odor emission and gut microbiome in growing-finishing pigs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157735. [PMID: 35926625 DOI: 10.1016/j.scitotenv.2022.157735] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/13/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
This study evaluated the effects of supplementing feed with arazyme and dietary carbohydrolases derived from invertebrate gut-associated symbionts on the noxious gas emissions, gut microbiota, and host-microbiome interactions of pigs. Here, 270 and 260 growing pigs were assigned to control and treatment groups, respectively. The tested feed additives contained a mixture of arazyme (2,500,000 Unit/kg) and synergetic enzymes, xylanase (200,000 Unit/kg) and mannanase (200,000 Unit/kg), derived from insect gut-associated symbionts in a 7.5:1:1 ratio. The control group was fed a basal diet and the treatment group was fed the basal diet supplemented with 0.1 % enzyme mixture (v/v) for 2 months. Odorous gases were monitored in ventilated air from tested houses. Fecal samples were collected from steel plate under the cage at the completion of the experiment to determine chemical composition, odor emissions, and bacterial communities. There was a significant decrease in the concentration of NH3 (22.5 vs. 11.2 ppm; P < 0.05), H2S (7.35 vs. 3.74 ppm; P < 0.05), trimethylamine (TMA) (0.066 vs. 0.001 ppm; P < 0.05), and p-cresol (0.004 ppm vs. 0 ppm; P < 0.05) at 56 d in treatment group compared with the control group. Moreover, fecal analysis results showed that exogenous enzyme supplementation caused a reduction in VFAs and indole content with approximately >60 % and 72.7 %, respectively. The result of gas emission analysis showed that NH3 (9.9 vs. 5.3 ppm; P < 0.05) and H2S (5.8 vs. 4.1 ppm; P < 0.05) were significantly reduced in the treatment group compared to the control group. The gut microbiota of the treatment group differed significantly from that of the control group, and the treatment group altered predicted metabolic pathways, including sulfur and nitrogen related metabolism, urea degradation. The results demonstrated that supplementing feed with arazyme with dietary carbohydrolases effectively controls noxious gas emissions and improves health and meat quality of pigs.
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Affiliation(s)
- Jong-Hoon Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Gwang-Pyo Ko
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Kwang-Hee Son
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Bon-Hwan Ku
- Insect Biotech Co. Ltd., Daejeon 34054, Republic of Korea
| | - Mi-Ae Bang
- Department of Animal Science, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Man-Jong Kang
- Department of Food Industry Research Center, Jeonnam Bioindustry Foundation, Naju 58275, Republic of Korea.
| | - Ho-Yong Park
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.
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Roslund MI, Puhakka R, Nurminen N, Oikarinen S, Siter N, Grönroos M, Cinek O, Kramná L, Jumpponen A, Laitinen OH, Rajaniemi J, Hyöty H, Sinkkonen A. Long-term biodiversity intervention shapes health-associated commensal microbiota among urban day-care children. ENVIRONMENT INTERNATIONAL 2021; 157:106811. [PMID: 34403882 DOI: 10.1016/j.envint.2021.106811] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/17/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND In modern urban environments children have a high incidence of inflammatory disorders, including allergies, asthma, and type1 diabetes. The underlying cause of these disorders, according to the biodiversity hypothesis, is an imbalance in immune regulation caused by a weak interaction with environmental microbes. In this 2-year study, we analyzed bacterial community shifts in the soil surface in day-care centers and commensal bacteria inhabiting the mouth, skin, and gut of children. We compared two different day-care environments: standard urban day-care centers and intervention day-care centers. Yards in the latter were amended with biodiverse forest floor vegetation and sod at the beginning of the study. RESULTS Intervention caused a long-standing increase in the relative abundance of nonpathogenic environmental mycobacteria in the surface soils. Treatment-specific shifts became evident in the community composition of Gammaproteobacteria, Negativicutes, and Bacilli, which jointly accounted for almost 40 and 50% of the taxa on the intervention day-care children's skin and in saliva, respectively. In the year-one skin swabs, richness of Alpha-, Beta-, and Gammaproteobacteria was higher, and the relative abundance of potentially pathogenic bacteria, including Haemophilus parainfluenzae, Streptococcus sp., and Veillonella sp., was lower among children in intervention day-care centers compared with children in standard day-care centers. In the gut, the relative abundance of Clostridium sensu stricto decreased, particularly among the intervention children. CONCLUSIONS This study shows that a 2-year biodiversity intervention shapes human commensal microbiota, including taxa that have been associated with immune regulation. Results indicate that intervention enriched commensal microbiota and suppressed the potentially pathogenic bacteria on the skin. We recommend future studies that expand intervention strategies to immune response and eventually the incidence of immune-mediated diseases.
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Affiliation(s)
- Marja I Roslund
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Niemenkatu 73, FI-15140 Lahti, Finland
| | - Riikka Puhakka
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Niemenkatu 73, FI-15140 Lahti, Finland
| | - Noora Nurminen
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland
| | - Nathan Siter
- Faculty of Built Environment, Tampere University, Korkeakoulunkatu 5, FI-33720 Tampere, Finland
| | - Mira Grönroos
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Niemenkatu 73, FI-15140 Lahti, Finland
| | - Ondřej Cinek
- Department of Pediatrics, Second Faculty of Medicine, Charles University, V Úvalu 84, Praha 5, 150 06 Prague, Czech Republic
| | - Lenka Kramná
- Department of Pediatrics, Second Faculty of Medicine, Charles University, V Úvalu 84, Praha 5, 150 06 Prague, Czech Republic
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan KS66506, KS, United States of America
| | - Olli H Laitinen
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland
| | - Juho Rajaniemi
- Faculty of Built Environment, Tampere University, Korkeakoulunkatu 5, FI-33720 Tampere, Finland
| | - Heikki Hyöty
- Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, FI-33520 Tampere, Finland
| | - Aki Sinkkonen
- Natural Resources Institute Finland, Turku, Finland.
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Anaerococcus faecalis sp. nov., Isolated from Swine Faeces. Curr Microbiol 2021; 78:2589-2594. [PMID: 33987692 DOI: 10.1007/s00284-021-02497-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/16/2021] [Indexed: 10/21/2022]
Abstract
An obligate anaerobic, Gram-stain-positive, non-spore forming, non-motile, catalase and oxidase-negative, coccoid-shaped bacterium designated AGMB00486T was isolated from swine faeces. The optimal growth of the isolate occurred at pH 8.0 and 37 ℃. Furthermore, the growth was observed in the presence of up to 4% (w/v) NaCl but not at salinity levels higher than 5%. The phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain AGMB00486T was a member of the genus Anaerococcus and that the isolate was most closely related to Anaerococcus vaginalis KCTC 15028T (96.7% 16S rRNA gene sequence similarity) followed by Anaerococcus hydrogenalis KCTC 15014T (96.7%) and Anaerococcus senegalensis KCTC 15435T (96.3%). Whole-genome sequence analysis determined that the DNA G+C content of strain AGMB00486T was 30.1 mol%, and the genome size, numbers of tRNA and rRNA genes were 2,268,866 bp, 47 and 8, respectively. The average nucleotide identity values between strain AGMB00486T and the three related type strains were 77.0, 77.4 and 77.2%, respectively. The major cellular fatty acids (> 10%) of strain AGMB00486T were C14:0, C16:0 and C16:0 DMA. Accordingly, these distinct phenotypic and phylogenetic properties revealed that strain AGMB00486T represents a novel species, for which the name Anaerococcus faecalis sp. nov. is proposed. The type strain is AGMB00486T (= KCTC 15945T = CCTCC AB 202009T).
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Morand A, Tall ML, Kuete Yimagou E, Ngom II, Lo CI, Cornu F, Tsimaratos M, Lagier JC, Levasseur A, Raoult D, Fournier PE. Anaerococcus urinimassiliensis sp. nov., a new bacterium isolated from human urine. Sci Rep 2021; 11:2684. [PMID: 33514860 PMCID: PMC7846727 DOI: 10.1038/s41598-021-82420-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 10/20/2020] [Indexed: 12/22/2022] Open
Abstract
To date there are thirteen species validly assigned to the genus Anaerococcus. Most of the species in this genus are anaerobic and of human origin. Anaerococcus urinimassiliensis sp. nov., strain Marseille-P2143T is member of family Peptoniphilaceae, which was isolated from the urine of a 17-year-old boy affected by autoimmune hepatitis and membranoproliferative glomerulonephritis using the culturomic approach. In the current study, a taxono-genomics method was employed to describe this new species. The strain Marseille-P2143T was gram positive cocci with translucent colonies on blood agar. Its genome was 2,189,509 bp long with a 33.5 mol% G + C content and exhibited 98.48% 16S rRNA similarity with Anaerococcus provencensis strain 9,402,080. When Anaerococcus urinomassiliensis strain Marseill-P2143T is compared with closely related species, the values ranged from 71.23% with A. hydrogenalis strain DSM 7454T (NZ_ABXA01000052.1) to 90.64% with A. provencensis strain 9402080T (NZ_HG003688.1). This strain has implemented the repertoire of known bacteria of the human urinary tract.
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Affiliation(s)
- Aurélie Morand
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France. .,Pédiatrie Spécialisée Et Médecine Infantile, Hôpital de La Timone, AP-HM, Marseille, France.
| | - Mamadou Lamine Tall
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Edmond Kuete Yimagou
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Issa Isaac Ngom
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Cheikh Ibrahima Lo
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Florent Cornu
- Pédiatrie Multidisciplinaire, Hôpital de La Timone, AP-HM, Marseille, France
| | - Michel Tsimaratos
- Pédiatrie Multidisciplinaire, Hôpital de La Timone, AP-HM, Marseille, France
| | - Jean-Christophe Lagier
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Anthony Levasseur
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Institut Universitaire de France (IUF), Paris, France
| | - Didier Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre-Edouard Fournier
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
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Clostridium massiliamazoniense sp. nov., New Bacterial Species Isolated from Stool Sample of a Volunteer Brazilian. Curr Microbiol 2020; 77:2008-2015. [PMID: 32613254 PMCID: PMC7415036 DOI: 10.1007/s00284-020-02099-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/18/2020] [Indexed: 12/20/2022]
Abstract
The study of the gut microbiota by the "culturomics concept" permitted us to isolate, from human stool sample, an unknown anaerobic bacterium within the genus Clostridium for which we propose the name Clostridium massiliamazoniense sp. nov. It was isolated from the fecal flora of a healthy 49-year-old Brazilian male. Here, we describe the characteristics of this organism and its complete genome sequencing and annotation. Clostridium massiliamazoniense sp. nov., ND2T (= CSURP1360 = DSMZ 27309) is a Gram-positive, obligate anaerobic member of Firmicutes with a 3,732,600 bp-long genome and a G+C content of 27.6%.
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Tall M, Pham T, Bellali S, Ngom I, Delerce J, Lo C, Raoult D, Fournier PE, Levasseur A. Anaerococcus marasmi sp. nov., a new bacterium isolated from human gut microbiota. New Microbes New Infect 2020; 35:100655. [PMID: 32211195 PMCID: PMC7082211 DOI: 10.1016/j.nmni.2020.100655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/10/2020] [Indexed: 12/22/2022] Open
Abstract
Anaerococcus marasmi sp. nov. strain Marseille-P3557T is a new species isolated from a stool of a Nigerian child with marasmus. The genome of Marseille-P3557T was 2 130 060 bp long (35.4% G + C content). The closest species based on 16S ribosomal RNA sequence was Anaerococcus prevotii strain 20548, with 97.6% sequence similarity. Considering phenotypic features and comparative genome studies, we propose the strain Marseille-P3557T as the type strain of Anaerococcus marasmi sp. nov., a new species within the genus Anaerococcus.
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Affiliation(s)
- M.L. Tall
- Aix-Marseille Université, Microbes, Evolution, Phylogeny and Infections, IRD, APHM, Faculté de Médecine, France
- IHU-Méditerranée Infection, France
| | - T.P.T. Pham
- Aix-Marseille Université, Microbes, Evolution, Phylogeny and Infections, IRD, APHM, Faculté de Médecine, France
- IHU-Méditerranée Infection, France
| | - S. Bellali
- Aix-Marseille Université, Microbes, Evolution, Phylogeny and Infections, IRD, APHM, Faculté de Médecine, France
- IHU-Méditerranée Infection, France
| | - I.I. Ngom
- Aix-Marseille Université, Microbes, Evolution, Phylogeny and Infections, IRD, APHM, Faculté de Médecine, France
- IHU-Méditerranée Infection, France
| | - J. Delerce
- Aix-Marseille Université, Microbes, Evolution, Phylogeny and Infections, IRD, APHM, Faculté de Médecine, France
- IHU-Méditerranée Infection, France
| | - C.I. Lo
- IHU-Méditerranée Infection, France
- Aix-Marseille Université, UMR VITROME, IRD, SSA, APHM, Faculté de Médecine, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, Microbes, Evolution, Phylogeny and Infections, IRD, APHM, Faculté de Médecine, France
- IHU-Méditerranée Infection, France
| | - P.-E. Fournier
- IHU-Méditerranée Infection, France
- Aix-Marseille Université, UMR VITROME, IRD, SSA, APHM, Faculté de Médecine, Marseille, France
| | - A. Levasseur
- Aix-Marseille Université, Microbes, Evolution, Phylogeny and Infections, IRD, APHM, Faculté de Médecine, France
- IHU-Méditerranée Infection, France
- Institut Universitaire de France (IUF), Paris, France
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Caputo A, Fournier PE, Raoult D. Genome and pan-genome analysis to classify emerging bacteria. Biol Direct 2019; 14:5. [PMID: 30808378 PMCID: PMC6390601 DOI: 10.1186/s13062-019-0234-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 02/14/2019] [Indexed: 12/21/2022] Open
Abstract
Background In the recent years, genomic and pan-genomic studies have become increasingly important. Culturomics allows to study human microbiota through the use of different culture conditions, coupled with a method of rapid identification by MALDI-TOF, or 16S rRNA. Bacterial taxonomy is undergoing many changes as a consequence. With the help of pan-genomic analyses, species can be redefined, and new species definitions generated. Results Genomics, coupled with culturomics, has led to the discovery of many novel bacterial species or genera, including Akkermansia muciniphila and Microvirga massiliensis. Using the genome to define species has been applied within the genus Klebsiella. A discontinuity or an abrupt break in the core/pan-genome ratio can uncover novel species. Conclusions Applying genomic and pan-genomic analyses to the reclassification of other bacterial species or genera will be important in the future of medical microbiology. The pan-genome is one of many new innovative tools in bacterial taxonomy. Reviewers This article was reviewed by William Martin, Eric Bapteste and James Mcinerney. Open peer review Reviewed by William Martin, Eric Bapteste and James Mcinerney.
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Affiliation(s)
- Aurélia Caputo
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | | | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.
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Dysgonomonas massiliensis sp. nov., a new species isolated from the human gut and its taxonogenomic description. Antonie van Leeuwenhoek 2019; 112:935-945. [DOI: 10.1007/s10482-019-01227-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/05/2019] [Indexed: 12/22/2022]
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10
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Bilen M, Mbogning Fonkou MD, Nguyen TT, Richez M, Daoud Z, Fournier PE, Raoult D, Cadoret F. Miniphocibacter massiliensis gen. nov., sp. nov., a new species isolated from the human gut and its taxono-genomics description. Microbiologyopen 2018; 8:e00735. [PMID: 30280501 PMCID: PMC6528615 DOI: 10.1002/mbo3.735] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/11/2018] [Accepted: 08/20/2018] [Indexed: 12/23/2022] Open
Abstract
With the aim of describing the human microbiota by the means of culture methods, culturomics was developed in order to target previously un‐isolated bacterial species and describe it via the taxono‐genomics approach. While performing a descriptive study of the human gut microbiota of the pygmy people, strain Marseille‐P4678T has been isolated from a stool sample of a healthy 39‐year‐old pygmy male. Cells of this strain were Gram‐positive cocci, spore‐forming, non‐motile, catalase‐positive and oxidase‐negative, and grow optimally at 37°C under anaerobic conditions. Its 16S rRNA gene sequence exhibited 89.69% of sequence similarity with Parvimonas micra strain 3119BT (NR 036934.1), its phylogenetically closest species with standing in nomenclature. The genome of strain Marseille‐P4678T is 2,083,161 long with 28.26 mol% of G+C content. Based on its phenotypic, biochemical, genotypic and proteomic profile, this bacterium was classified as a new bacterial genus and species Miniphocibacter massiliensis gen. nov., sp. nov. with the type strain Marseille‐P4678T.
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Affiliation(s)
- Melhem Bilen
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Clinical Microbiology Department, Faculty of Medicine and Medical Sciences, University of Balamand, Amioun, Lebanon
| | | | - Thi T Nguyen
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Magali Richez
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Ziad Daoud
- Clinical Microbiology Department, Faculty of Medicine and Medical Sciences, University of Balamand, Amioun, Lebanon
| | - Pierre E Fournier
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Frédéric Cadoret
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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11
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Bilen M, Beye M, Mbogning Fonkou MD, Khelaifia S, Cadoret F, Armstrong N, Nguyen TT, Delerce J, Daoud Z, Raoult D, Fournier PE. Genomic and phenotypic description of the newly isolated human species Collinsella bouchesdurhonensis sp. nov. Microbiologyopen 2018; 7:e00580. [PMID: 29900684 PMCID: PMC6182551 DOI: 10.1002/mbo3.580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 12/19/2022] Open
Abstract
Using culturomics, a recently developed strategy based on diversified culture conditions for the isolation of previously uncultured bacteria, we isolated strain Marseille‐P3296T from a fecal sample of a healthy pygmy female. A multiphasic approach, taxono‐genomics, was used to describe the major characteristics of this anaerobic and gram‐positive bacillus that is unable to sporulate and is not motile. The genome of this bacterium is 1,878,572 bp‐long with a 57.94 mol% G + C content. On the basis of these characteristics and after comparison with its closest phylogenetic neighbors, we are confident that strain Marseille‐P3296T (=CCUG 70328 = CSUR P3296) is the type strain of a novel species for which we propose the name Collinsella bouchesdurhonensis sp. nov.
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Affiliation(s)
- Melhem Bilen
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France.,Clinical Microbiology Department, Faculty of Medicine and Medical sciences, University of Balamand, Amioun, Lebanon
| | - Mamadou Beye
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Maxime Descartes Mbogning Fonkou
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Saber Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Frédéric Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Nicholas Armstrong
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Thi Tien Nguyen
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Jérémy Delerce
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - Ziad Daoud
- Clinical Microbiology Department, Faculty of Medicine and Medical sciences, University of Balamand, Amioun, Lebanon
| | - Didier Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
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12
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Bilen M, Fonkou MDM, Tomei E, Armstrong N, Bittar F, Lagier JC, Daoud Z, Fournier PE, Raoult D, Cadoret F. Eggerthella timonensis sp. nov, a new species isolated from the stool sample of a pygmy female. Microbiologyopen 2018; 7:e00575. [PMID: 29900700 PMCID: PMC6182555 DOI: 10.1002/mbo3.575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 12/19/2022] Open
Abstract
Eggerthella timonensis strain Marseille-P3135 is a new bacterial species, isolated from the stool sample of a healthy 8-year-old pygmy female. This strain (LT598568) showed a 16S rRNA sequence similarity of 96.95% with its phylogenetically closest species with standing in nomenclature Eggerthella lenta strain DSM 2243 (AF292375). This bacterium is a nonspore forming, Gram-positive, nonmotile rod with catalase but no oxidase activity. Its genome is 3,916,897 bp long with 65.17 mol% of G + C content. Of the 3,371 predicted genes, 57 were RNAs and 3,314 were protein-coding genes. Here, we report the main phenotypic, biochemical, and genotypic characteristics of E. timonensis strain Marseille-P3135 (=CSUR P3135, =CCUG 70327); ti.mo.nen'sis, N.L. masc. adj., with timonensis referring to La Timone, which is the name of the hospital in Marseille (France) where this work was performed). Strain is a nonmotile Gram-positive rod, unable to sporulate, oxidase negative, and catalase positive. It grows under anaerobic conditions between 25°C and 42°C but optimally at 37°C.
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Affiliation(s)
- Melhem Bilen
- URMITE UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille Cedex, France.,Clinical Microbiology Department, Faculty of Medicine and Medical sciences, University of Balamand, Amioun, Lebanon
| | - Maxime Descartes Mbogning Fonkou
- URMITE UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille Cedex, France
| | - Enora Tomei
- URMITE UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille Cedex, France
| | - Nicholas Armstrong
- URMITE UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille Cedex, France
| | - Fadi Bittar
- URMITE UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille Cedex, France
| | - Jean-Christophe Lagier
- URMITE UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille Cedex, France
| | - Ziad Daoud
- Clinical Microbiology Department, Faculty of Medicine and Medical sciences, University of Balamand, Amioun, Lebanon
| | - Pierre-Edouard Fournier
- URMITE UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille Cedex, France
| | - Didier Raoult
- URMITE UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille Cedex, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Frédéric Cadoret
- URMITE UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille Cedex, France
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13
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Mathlouthi N, Traore S, Cimmino T, Khelaifia S, Nguyen T, Cadoret F, Couderc C, Raoult D, Rolain JM. Genome sequence and description of Mobilicoccus massiliensis sp. nov. isolated from the stool of a Nigerian boy with kwashiorkor. New Microbes New Infect 2017; 20:18-24. [PMID: 29158905 PMCID: PMC5682880 DOI: 10.1016/j.nmni.2017.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 08/30/2017] [Accepted: 08/31/2017] [Indexed: 11/08/2022] Open
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.
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Affiliation(s)
| | | | | | | | | | | | | | | | - J.-M. Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, Marseille, France
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14
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Dione N, Rathored J, Tomei E, Lagier JC, Khelaifia S, Robert C, Bretelle F, Raoult D, Fournier PE, Fenollar F. Dakarella massiliensis gen. nov., sp. nov., strain ND3 T: a new bacterial genus isolated from the female genital tract. New Microbes New Infect 2017; 18:38-46. [PMID: 28603641 PMCID: PMC5454129 DOI: 10.1016/j.nmni.2017.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/26/2017] [Accepted: 05/09/2017] [Indexed: 11/25/2022] Open
Abstract
Strain ND3T was isolated from the genital tract of a 28-year-old woman with bacterial vaginosis. This strain exhibited a 16S rRNA gene sequence similarity of 92.4% with Sutterella wadsworthensis, the phylogenetically closest species with standing in nomenclature. Strain ND3T was a strictly anaerobic Gram-negative rod and member of the family Sutterellaceae. It exhibited a genome of 2 476 884 bp containing 2175 protein-coding and 62 RNA genes. On the basis of these data, we propose the creation of ‘Dakarella massiliensis’ sp. nov. with strain ND3T (= CSUR P1938 = DSM 100447) as the type strain.
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Affiliation(s)
- N Dione
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - J Rathored
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - E Tomei
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - J-C Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - S Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - C Robert
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - F Bretelle
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France.,Department of Gynecology and Obstetrics, Gynépole, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Aix-Marseille Université, Marseille, France
| | - D Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P-E Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - F Fenollar
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
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15
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Khelaifia S, Lagier JC, Bibi F, Azhar EI, Croce O, Padmanabhan R, Jiman-Fatani AA, Yasir M, Robert C, Andrieu C, Fournier PE, Raoult D. Microbial Culturomics to Map Halophilic Bacterium in Human Gut: Genome Sequence and Description of Oceanobacillus jeddahense sp. nov. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 20:248-58. [PMID: 27093109 DOI: 10.1089/omi.2016.0004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Culturomics is a new omics subspecialty to map the microbial diversity of human gut, coupled with a taxono-genomic strategy. We report here the description of a new bacterial species using microbial culturomics: strain S5T, (= CSUR P1091=DSM 28586) isolated from a stool specimen of a 25-year-old obese patient from Saudi Arabia. The strain S5T was a Gram-positive, strictly aerobic rod, which was motile by a polar flagellum, spore-forming, and exhibited catalase and oxidase activities. It grows optimally at 37°C, with a pH of 7.5 and 10% of NaCl. 16S rRNA gene-based identification revealed that strain S5T has 98.6% 16S rRNA sequence similarity with the reference O. oncorhynchi, phylogenetically the closest validated Oceanobacillus species. Here, we further describe the phenotypic characteristics of this organism and its complete genome sequence and annotation. The 5,388,285 bp long genome exhibits a G+C content of 37.24% and contains 5109 protein-coding genes and 198 RNA genes. Based on the characteristics reported here, we propose classifying this novel bacterium as representative of a new species belonging to the genus Oceanobacillus, Oceanobacillus jeddahense sp. nov. In a broader context, it is noteworthy that halophilic bacteria have long been overlooked in the human gut, and their role in human health and disease has not yet been investigated. This study thus further underscores the usefulness of the culturomics approach exploring the bacterial diversity of the gut.
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Affiliation(s)
- Saber Khelaifia
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Jean-Christophe Lagier
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Fehmida Bibi
- 2 Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Esam Ibraheem Azhar
- 2 Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia .,3 Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Olivier Croce
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Roshan Padmanabhan
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Asif Ahmad Jiman-Fatani
- 4 Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Muhammad Yasir
- 2 Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Catherine Robert
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Claudia Andrieu
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Pierre-Edouard Fournier
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca
| | - Didier Raoult
- 1 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS (UMR 7278), IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université , Marseille, Franca.,2 Special Infectious Agents Unit, King Fahd Medical Research Center, Faculty of Medicine, King Abdulaziz University , Jeddah, Saudi Arabia
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16
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Mailhe M, Ricaboni D, Vitton V, Benezech A, Dubourg G, Michelle C, Andrieu C, Armstrong N, Bittar F, Fournier PE, Raoult D, Million M. Noncontiguous finished genome sequence and description of Fusobacterium massiliense sp. nov. isolated from human duodenum. New Microbes New Infect 2016; 16:3-12. [PMID: 28116104 PMCID: PMC5225283 DOI: 10.1016/j.nmni.2016.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/01/2016] [Indexed: 11/13/2022] Open
Abstract
The strain Marseille-P2749T (= CSUR P2749 = DSM 103085) was isolated as part of culturomics study from a liquid duodenum sample from a French man. Bacterial cells were Gram-negative bacilli, fusiform shaped and non–spore forming, and they grew in microaerophilic and anaerobic atmosphere. Its genome is 1 809 169 bp long and contains 1646 protein-coding genes. The DNA G+C content was 27.33 mol%. This strain exhibited a 95.9% sequence similarity with Fusobacterium periodonticum, the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2749T is suggested to be a novel species belonging to the genus Fusobacterium, for which the name Fusobacterium massiliense sp. nov. is proposed.
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Affiliation(s)
- M Mailhe
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D Ricaboni
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France; Département des sciences cliniques et biomédicales, Luigi Sacco, Division des Maladies Infectieuses III, Université de Milan, Milan, Italy
| | - V Vitton
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - A Benezech
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
| | - G Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - C Michelle
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - C Andrieu
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - N Armstrong
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - F Bittar
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - D Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M Million
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
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17
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Mourembou G, Yasir M, Azhar EI, Lagier JC, Bibi F, Jiman-Fatani AA, Helmy N, Robert C, Rathored J, Fournier PE, Raoult D, Million M. Rise of Microbial Culturomics: Noncontiguous Finished Genome Sequence and Description of Beduini massiliensis gen. nov., sp. nov. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:766-76. [PMID: 26669711 DOI: 10.1089/omi.2015.0143] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Microbial culturomics is a new field of omics sciences that examines the bacterial diversity of human gut coupled with a taxono-genomic strategy. Using microbial culturomics, we report here for the first time a novel Gram negative, catalase- and oxidase-negative, strict anaerobic bacilli named Beduini massiliensis gen. nov., sp nov. strain GM1 (= CSUR P1440 = DSM 100188), isolated from the stools of a female nomadic Bedouin from Saudi Arabia. With a length of 2,850,586 bp, the Beduini massiliensis genome exhibits a G + C content of 35.9%, and contains 2819 genes (2744 protein-coding and 75 RNA genes including 57 tRNA and 18 rRNA genes). It is composed of 6 scaffolds (composed of 6 contigs). A total of 1859 genes (67.75%) were assigned a putative function (by COGs or by NR blast). At least 1457 (53%) orthologous proteins were not shared with the closest phylogenetic species. 274 genes (10.0%) were identified as ORFans. These results show that microbial culturomics can dramatically improve the characterization of the human microbiota repertoire, deciphering new bacterial species and new genes. Further studies will clarify the geographic specificity and the putative role of these new microbes and their related functional genetic content in health and disease. Microbial culturomics is an emerging frontier of omics systems sciences and integrative biology and thus, warrants further consideration as part of the postgenomics methodology toolbox.
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Affiliation(s)
- Gaël Mourembou
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France .,2 Regional Doctoral School of Central Africa , Franceville, Gabon
| | - Muhammad Yasir
- 3 Special Infectious Agents Unit, King Fahd Medical Research Center , King Abdulaziz University , Jeddah, Saudi Arabia
| | - Esam Ibraheem Azhar
- 3 Special Infectious Agents Unit, King Fahd Medical Research Center , King Abdulaziz University , Jeddah, Saudi Arabia .,4 Department of Medical Laboratory Technology, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Jean Christophe Lagier
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Fehmida Bibi
- 3 Special Infectious Agents Unit, King Fahd Medical Research Center , King Abdulaziz University , Jeddah, Saudi Arabia
| | - Asif Ahmad Jiman-Fatani
- 5 Department of Medical Microbiology and Parasitology, King Abdulaziz University , Jeddah, Saudi Arabia
| | - Nayel Helmy
- 6 Department of Obstetrics and Gynaecology, Suliman Fageeh Hospital , Jeddah, Saudi Arabia
| | - Catherine Robert
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Jaishriram Rathored
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Pierre-Edouard Fournier
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Didier Raoult
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France .,3 Special Infectious Agents Unit, King Fahd Medical Research Center , King Abdulaziz University , Jeddah, Saudi Arabia
| | - Matthieu Million
- 1 Aix Marseille University , URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
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Mourembou G, Rathored J, Lekana-Douki JB, Ndjoyi-Mbiguino A, Khelaifia S, Robert C, Armstrong N, Raoult D, Fournier PE. Description of Gabonibacter massiliensis gen. nov., sp. nov., a New Member of the Family Porphyromonadaceae Isolated from the Human Gut Microbiota. Curr Microbiol 2016; 73:867-877. [PMID: 27628331 DOI: 10.1007/s00284-016-1137-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 09/08/2016] [Indexed: 12/19/2022]
Abstract
The identification of human-associated bacteria is very important to control infectious diseases. In recent years, we diversified culture conditions in a strategy named culturomics, and isolated more than 100 new bacterial species and/or genera. Using this strategy, strain GM7, a strictly anaerobic gram-negative bacterium was recently isolated from a stool specimen of a healthy Gabonese patient. It is a motile coccobacillus without catalase and oxidase activities. The genome of Gabonibacter massiliensis is 3,397,022 bp long with 2880 ORFs and a G+C content of 42.09 %. Of the predicted genes, 2,819 are protein-coding genes, and 61 are RNAs. Strain GM7 differs from the closest genera within the family Porphyromonadaceae both genotypically and in shape and motility. Thus, we propose that strain GM7T (=CSUR P2336 = DSM 101039) is the type strain of the new genus Gabonibacter gen. nov. and the new species G. massiliensis gen. nov., sp. nov.
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Affiliation(s)
- Gaël Mourembou
- URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, Marseille, France.,Ecole Doctorale Régionale d'Afrique Centrale, B.P. 876, Franceville, Gabon
| | - Jaishriram Rathored
- URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, Marseille, France
| | - Jean Bernard Lekana-Douki
- Unité de Parasitologie Médicale (UPARAM), CIRMF B.P. 769, Franceville, Gabon.,Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Sciences de la Santé, B.P. 4009, Libreville, Gabon
| | - Angélique Ndjoyi-Mbiguino
- Département de Microbiologie, Laboratoire national de référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, B.P. 4009, Libreville, Gabon
| | - Saber Khelaifia
- URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, Marseille, France
| | - Catherine Robert
- URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, Marseille, France
| | - Nicholas Armstrong
- URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, Marseille, France
| | - Didier Raoult
- URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, 27 Bd Jean Moulin, Marseille, France.
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19
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Seck E, Traore S, Khelaifia S, Beye M, Michelle C, Couderc C, Brah S, Fournier PE, Raoult D, Dubourg G. Tessaracoccus massiliensis sp. nov., a new bacterial species isolated from the human gut. New Microbes New Infect 2016; 13:3-12. [PMID: 27358740 PMCID: PMC4916054 DOI: 10.1016/j.nmni.2016.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/28/2016] [Accepted: 05/03/2016] [Indexed: 11/22/2022] Open
Abstract
A new Actinobacterium, designated Tessaracoccus massiliensis type strain SIT-7(T) (= CSUR P1301 = DSM 29060), have been isolated from a Nigerian child with kwashiorkor. It is a facultative aerobic, Gram positive, rod shaped, non spore-forming, and non motile bacterium. Here, we describe the genomic and phenotypic characteristics of this isolate. Its 3,212,234 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 67.81% and contains 3,058 protein-coding genes and 49 RNA genes.
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Affiliation(s)
- E. Seck
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - S.I. Traore
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - S. Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - M. Beye
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - C. Michelle
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - C. Couderc
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - S. Brah
- Hôpital National de Niamey, Niamey, Niger
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - G. Dubourg
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Faculté de médecine, Marseille, France
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20
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Tidjani Alou M, Khelaifia S, Michelle C, Andrieu C, Armstrong N, Bittar F, Sokhna C, Diallo A, Fournier PE, Raoult D, Million M. Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition. Anaerobe 2016; 40:85-94. [PMID: 27328611 DOI: 10.1016/j.anaerobe.2016.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 01/04/2023]
Abstract
Anaerococcus rubiinfantis sp. nov. strain mt16(T) is a new species within the genus Anaerococcus, which was isolated by the culturomics approach from the gut microbiota of an infant suffering from kwashiorkor. A phenotypic, biochemical and proteomic description of this strain is hereby presented alongside a complete annotation of its genome. This strictly anaerobic species forms Gram-positive non-sporeforming cocci. The major fatty acid was hexadecanoic acid. The phylogenetic analysis of strain mt16(T) showed a 97.9% similarity level with Anaerococcus vaginalis, the closest validly published species. Its genome is 1,929,161 bp long with 29.5% G + C content and contains 1808 protein-coding genes and 56 RNA genes, among which are six rRNA genes. Genomic analysis identified 41/1864 coding genes as ORFans (2.2%) and at least 620/1808 (34.9%) orthologous proteins which are not shared with the closest phylogenetic species. We believe that the extension of the human anaerobic gut compendium by culturomics is one of the first steps that will improve the understanding of the links between the microbiome and health or disease.
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Affiliation(s)
- Maryam Tidjani Alou
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Saber Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Caroline Michelle
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Claudia Andrieu
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Nicholas Armstrong
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Fadi Bittar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Cheikh Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - Aldiouma Diallo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France; Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Campus Commun UCAD-IRD of Hann, Dakar, Senegal; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Matthieu Million
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France.
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21
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Caputo A, Lagier J, Azza S, Robert C, Mouelhi D, Fournier P, Raoult D. Microvirga massiliensis sp. nov., the human commensal with the largest genome. Microbiologyopen 2016; 5:307-22. [PMID: 26749561 PMCID: PMC4831475 DOI: 10.1002/mbo3.329] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 11/12/2015] [Accepted: 11/19/2015] [Indexed: 11/09/2022] Open
Abstract
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.
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Affiliation(s)
- Aurélia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
| | - Jean‐Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
| | - Saïd Azza
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
| | - Donia Mouelhi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
| | - Pierre‐Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales ÉmergentesCNRSUMR 7278 – IRD 198Faculté de médecineAix‐Marseille Université27 Boulevard Jean Moulin13385Marseille Cedex 05France
- Special Infectious Agents UnitKing Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia
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22
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Tidjani Alou M, Rathored J, Lagier JC, Khelaifia S, Labas N, Sokhna C, Diallo A, Raoult D, Dubourg G. Massilibacterium senegalense gen. nov., sp. nov., a new bacterial genus isolated from the human gut. New Microbes New Infect 2016; 10:101-11. [PMID: 26933503 PMCID: PMC4765772 DOI: 10.1016/j.nmni.2016.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/11/2016] [Accepted: 01/14/2016] [Indexed: 01/15/2023] Open
Abstract
Massilibacterium senegalense gen. nov., sp. nov., strain mt8(T), is the type strain of Massilibacterium gen. nov., a new genus within the Bacillaceae family. This Gram-negative facultative anaerobic rod was isolated from the gut microbiota of a severely malnourished boy. Its phenotypic description is hereby presented with a complete annotation of its genome sequence. This genome is 5 697 950 bp long and contains 5615 protein-coding genes and 178 RNA genes, among which are 40 rRNA genes.
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Affiliation(s)
- M. Tidjani Alou
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - J. Rathored
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - J.-C. Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - S. Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - N. Labas
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - C. Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - A. Diallo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - D. Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - G. Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
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23
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Dione N, Sankar S, Lagier JC, Khelaifia S, Michele C, Armstrong N, Richez M, Abrahão J, Raoult D, Fournier PE. Genome sequence and description of Anaerosalibacter massiliensis sp. nov. New Microbes New Infect 2016; 10:66-76. [PMID: 26937282 PMCID: PMC4753391 DOI: 10.1016/j.nmni.2016.01.002] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/30/2015] [Accepted: 01/04/2016] [Indexed: 01/09/2023] Open
Abstract
Anaerosalibacter massiliensis sp. nov. strain ND1(T) (= 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.
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Affiliation(s)
- N. Dione
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - S.A. Sankar
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - S. Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - C. Michele
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - N. Armstrong
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - M. Richez
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
| | - J. Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de Médecine, Marseille, France
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24
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Dubourg G, Sankar SA, Rathored J, Lagier JC, Robert C, Couderc C, Papazian L, Raoult D, Fournier PE. Noncontiguous finished genome sequence and description of Nocardioides massiliensis sp. nov. GD13(T). New Microbes New Infect 2016; 10:47-57. [PMID: 27257488 PMCID: PMC4877605 DOI: 10.1016/j.nmni.2016.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 12/31/2015] [Accepted: 01/04/2016] [Indexed: 11/24/2022] Open
Abstract
Nocardioides massiliensis sp. nov strain GD13T is the type strain of N. massiliensis sp. nov., a new species within the genus Nocardioides. This strain was isolated from the faeces of a 62-year-old man admitted to intensive care for Guillain-Barré syndrome. Nocardioides massiliensis is a strictly aerobic Gram-positive rod. Herein we describe the features of this bacterium, together with the complete genome sequence and annotation. The 4 006 620 bp long genome contains 4132 protein-coding and 47 RNA genes.
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Affiliation(s)
- G Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - S A Sankar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - J Rathored
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - J-C Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - C Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - C Couderc
- Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - L Papazian
- Service de Réanimation Médicale-Détresse Respiratoires et Infections Sévères, Hôpital Nord, Marseille, France
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - P-E Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Marseille, France
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25
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Mourembou G, Rathored J, Lekana-Douki J, Ndjoyi-Mbiguino A, Fenollar F, Michelle C, Fournier PE, Raoult D, Lagier JC. Noncontiguous finished genome sequence and description of Kallipyga gabonensis sp. nov. New Microbes New Infect 2016; 9:15-23. [PMID: 26862430 PMCID: PMC4706609 DOI: 10.1016/j.nmni.2015.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 11/23/2022] Open
Abstract
Taxonogenomics coupled with culturomics promotes the isolation and characterization of bacteria. Kallipyga gabonensis sp. nov. strain GM4 is a strictly anaerobic, Gram-positive, and non motile coccus isolated from the stool of a Gabonese male teenager. The genome is 1,621,211 bp long with 50.01% G+C content and two scaffolds. Of the 1,536 predicted genes, 1,475 were protein-coding genes and 61 were RNA genes. A total of 931 genes were assigned a putative function, and 79 genes were identified as ORFans.
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Affiliation(s)
- G. Mourembou
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Ecole Doctorale Régionale d’Afrique Centrale, Franceville, Gabon
| | - J. Rathored
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - J.B. Lekana-Douki
- Unité de Parasitologie Médicale (UPARAM), CIRMF, Franceville, Gabon
- Département de Parasitologie Mycologie et de Médecine Tropicale, Laboratoire national de référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
| | - A. Ndjoyi-Mbiguino
- Département de Microbiologie, Laboratoire national de référence IST/sida, Faculté de Médecine, Université des Sciences de la Santé, Libreville, Gabon
| | - F. Fenollar
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - C. Michelle
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - P.-E. Fournier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - D. Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.-C. Lagier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
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Mourembou G, Rathored J, Ndjoyi-Mbiguino A, Lekana-Douki J, Fenollar F, Robert C, Fournier PE, Raoult D, Lagier J. Noncontiguous finished genome sequence and description of Gabonia massiliensis gen. nov., sp. nov. New Microbes New Infect 2016; 9:35-44. [PMID: 26862432 PMCID: PMC4706602 DOI: 10.1016/j.nmni.2015.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 11/28/2022] Open
Abstract
Culturomics coupled with taxonogenomics is currently used to isolate and characterize new bacteria. Here we describe the features and complete genome sequence of Gabonia massiliensis strain GM3, an anaerobic Gram negative, non-spore-forming and catalase-positive bacillus isolated from a stool specimen of a healthy Gabonese male youth. Belonging to a new genus called Gabonia, it exhibits a genome of 4 261 752 bp including 37.9% GC content and 3,288 predicted genes.
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Affiliation(s)
- G. Mourembou
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Ecole Doctorale Régionale d'Afrique Centrale, Gabon
| | - J. Rathored
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - A. Ndjoyi-Mbiguino
- Département de Microbiologie, Laboratoire National de référence IST/sida, Faculté de Médecine, Gabon
| | - J.B. Lekana-Douki
- Unité de Parasitologie Médicale (UPARAM) CIRMF, Franceville, Gabon
- Département de Parasitologie Mycologie et de Médecine Tropicale, Université des Sciences de la Santé B.P., Libreville, Gabon
| | - F. Fenollar
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - C. Robert
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - P.-E. Fournier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - D. Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.C. Lagier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
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27
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Fournier PE, Lagier JC, Dubourg G, Raoult D. From culturomics to taxonomogenomics: A need to change the taxonomy of prokaryotes in clinical microbiology. Anaerobe 2015; 36:73-8. [DOI: 10.1016/j.anaerobe.2015.10.011] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 10/06/2015] [Accepted: 10/23/2015] [Indexed: 01/07/2023]
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Veloo ACM, de Vries ED, Jean-Pierre H, van Winkelhoff AJ. Anaerococcus nagyae sp. nov., isolated from human clinical specimens. Anaerobe 2015; 38:111-115. [PMID: 26639871 DOI: 10.1016/j.anaerobe.2015.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 11/20/2015] [Accepted: 11/23/2015] [Indexed: 11/16/2022]
Abstract
We describe a new Anaerococcus species isolated from human clinical specimens. Analyses of 16S rRNA gene sequences of three strains showed <98% similarity with its closest relative Anaerococcus octavius. Phylogenetically the isolated strains form a cluster and can be differentiated from other species of the genus Anaerococcus based on its phenotypic characteristics and its MALDI-TOF MS profile. We propose the name Anaerococcus nagyae, with A. nagyae DSM101193 (accession number KU043522) as the type strain.
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Affiliation(s)
- A C M Veloo
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands.
| | - E D de Vries
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands
| | - H Jean-Pierre
- Centre Hospitalier Universitaire de Montpellier, Hôpital Arnaud de Villeneuve, Laboratoire de Bactériologie, 371 Avenue Du Doyen Gaston Giraud, Montpellier Cedex 5 34295, France; Université Montpellier 1, UMR5119 ECOSYM, Equipe Pathogènes et Environnements, U.F.R des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, Montpellier Cedex 5 34093, France
| | - A J van Winkelhoff
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Dentistry and Oral Hygiene, The Netherlands
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Tidjiani Alou M, Rathored J, Khelaifia S, Michelle C, Brah S, Diallo B, Raoult D, Lagier JC. Bacillus rubiinfantis sp. nov. strain mt2(T), a new bacterial species isolated from human gut. New Microbes New Infect 2015; 8:51-60. [PMID: 27076912 PMCID: PMC4815707 DOI: 10.1016/j.nmni.2015.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/01/2015] [Accepted: 09/07/2015] [Indexed: 11/28/2022] Open
Abstract
Bacillus rubiinfantis sp. nov. strain mt2(T) is the type strain of B. rubiinfantis sp. nov., isolated from the fecal flora of a child with kwashiorkor in Niger. It is Gram-positive facultative anaerobic rod belonging to the Bacillaceae family. We describe the features of this organism alongside the complete genome sequence and annotation. The 4 311 083 bp long genome (one chromosome but no plasmid) contains 4028 protein-coding gene and 121 RNA genes including nine rRNA genes.
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Affiliation(s)
- M. Tidjiani Alou
- Faculté de médecine, Unité des Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, Inserm 1095, Aix-Marseille Université, Marseille, France
| | - J. Rathored
- Faculté de médecine, Unité des Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, Inserm 1095, Aix-Marseille Université, Marseille, France
| | - S. Khelaifia
- Faculté de médecine, Unité des Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, Inserm 1095, Aix-Marseille Université, Marseille, France
| | - C. Michelle
- Faculté de médecine, Unité des Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, Inserm 1095, Aix-Marseille Université, Marseille, France
| | - S. Brah
- Hopital National de Niamey, Niamey, Niger
| | - B.A. Diallo
- Laboratoire de microbiologie, département de biologie, Université Abdou Moumouni de Niamey, Niamey, Niger
| | - D. Raoult
- Faculté de médecine, Unité des Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, Inserm 1095, Aix-Marseille Université, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.-C. Lagier
- Faculté de médecine, Unité des Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, Inserm 1095, Aix-Marseille Université, Marseille, France
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30
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Seck E, Rathored J, Khelaifia S, Croce O, Robert C, Couderc C, Di Pinto F, Sokhna C, Raoult D, Lagier JC. Virgibacillus senegalensis sp. nov., a new moderately halophilic bacterium isolated from human gut. New Microbes New Infect 2015; 8:116-26. [PMID: 26693281 PMCID: PMC4660226 DOI: 10.1016/j.nmni.2015.09.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/23/2015] [Accepted: 09/24/2015] [Indexed: 11/23/2022] Open
Abstract
Virgibacillus senegalensis SK-1(T) (= 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.
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Affiliation(s)
- E. Seck
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - J. Rathored
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - S. Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - O. Croce
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - C. Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - C. Couderc
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - F. Di Pinto
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - C. Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - D. Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.-C. Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
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31
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Tidjani Alou M, Rathored J, Traore S, Khelaifia S, Michelle C, Brah S, Diallo B, Raoult D, Lagier JC. Bacillus niameyensis sp. nov., a new bacterial species isolated from human gut. New Microbes New Infect 2015; 8:61-9. [PMID: 27076913 PMCID: PMC4815930 DOI: 10.1016/j.nmni.2015.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/13/2015] [Accepted: 09/14/2015] [Indexed: 10/29/2022] Open
Abstract
Bacillus niameyensis sp. nov. strain SIT3(T) (= CSUR P1266 = DSM 29725) is the type strain of B. niameyensis sp. nov. This Gram-positive strain was isolated from the digestive flora of a child with kwashiorkor and is a facultative anaerobic rod and a member of the Bacillaceae family. This organism is hereby described alongside its complete genome sequence and annotation. The 4 286 116 bp long genome (one chromosome but no plasmid) contains 4130 protein-coding and 66 RNA genes including five rRNA genes.
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Affiliation(s)
- M. Tidjani Alou
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
| | - J. Rathored
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
| | - S.I. Traore
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
| | - S. Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
| | - C. Michelle
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
| | - S. Brah
- Hopital National de Niamey, Niger
| | - B.A. Diallo
- Laboratoire de Microbiologie, Département de Biologie, Université Abdou Moumouni de Niamey, Niamey, Niger
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J.-C. Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, Marseille, France
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32
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Dubourg G, Cimmino T, Senkar SA, Lagier JC, Robert C, Flaudrops C, Brouqui P, Raoult D, Fournier PE, Rolain JM. Noncontiguous finished genome sequence and description of Paenibacillus antibioticophila sp. nov. GD11(T), the type strain of Paenibacillus antibioticophila. New Microbes New Infect 2015; 8:137-47. [PMID: 27257493 PMCID: PMC4877408 DOI: 10.1016/j.nmni.2015.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/07/2015] [Accepted: 10/07/2015] [Indexed: 11/22/2022] Open
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.
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Affiliation(s)
- G Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France
| | - T Cimmino
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - S A Senkar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - J-C Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France
| | - C Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - C Flaudrops
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - P Brouqui
- Service des Maladies Infectieuses et Tropicales. Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, France
| | - D Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - P-E Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France
| | - J-M Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France; Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, University, Hospital Centre Timone, Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, France
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Sankar SA, Rathored J, Metidji S, Lagier JC, Khelaifia S, Labas N, Musso D, Raoult D, Fournier PE. Clostridium polynesiense sp. nov., a new member of the human gut microbiota in French Polynesia. Anaerobe 2015; 36:79-87. [PMID: 26485191 DOI: 10.1016/j.anaerobe.2015.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/07/2015] [Accepted: 10/10/2015] [Indexed: 11/17/2022]
Abstract
Strain MS1, a Gram-positive, obligately anaerobic, motile and spore-forming rod belonging to the Clostridium genus, was isolated from the feces of a healthy Polynesian male living in French Polynesia. The temperature range for growth was 30-45 °C. We sequenced its complete genome and studied its phenotypic characteristics. The 3,560,738-bp long genome (one chromosome, no plasmid, G + C content 34%) contained 3535 protein-coding and 70 RNA genes. Strain MS1 exhibited a 98.24% 16S rRNA similarity with Clostridium amylolyticum, the phylogenetically closest species. When compared with other Clostridium species with standing in nomenclature, it had an average genomic similarity of 68.8-70%, a unique MALDI-TOF spectrum, and differed in nitrate reduction, motility and L-arabinose and D-lactose metabolism with most of the closest species. Therefore, strain MS1 is sufficiently distinct from type strains of the genus Clostridium to represent a novel species within this genus, for which the name Clostridium polynesiense sp. nov. is proposed. The type strain of C. polynesiense is MS1(T) (= CSUR P630 = DSM 27072).
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Affiliation(s)
- Senthil Alias Sankar
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Jaishriram Rathored
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Sarah Metidji
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Saber Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Noemie Labas
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Didier Musso
- Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Didier Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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Hugon P, Dufour JC, Colson P, Fournier PE, Sallah K, Raoult D. A comprehensive repertoire of prokaryotic species identified in human beings. THE LANCET. INFECTIOUS DISEASES 2015; 15:1211-1219. [PMID: 26311042 DOI: 10.1016/s1473-3099(15)00293-5] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 02/17/2015] [Accepted: 02/27/2015] [Indexed: 02/07/2023]
Abstract
The compilation of the complete prokaryotic repertoire associated with human beings as commensals or pathogens is a major goal for the scientific and medical community. The use of bacterial culture techniques remains a crucial step to describe new prokaryotic species. The large number of officially acknowledged bacterial species described since 1980 and the recent increase in the number of recognised pathogenic species have highlighted the absence of an exhaustive compilation of species isolated in human beings. By means of a thorough investigation of several large culture databases and a search of the scientific literature, we built an online database containing all human-associated prokaryotic species described, whether or not they had been validated and have standing in nomenclature. We list 2172 species that have been isolated in human beings. They were classified in 12 different phyla, mostly in the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes phyla. Our online database is useful for both clinicians and microbiologists and forms part of the Human Microbiome Project, which aims to characterise the whole human microbiota and help improve our understanding of the human predisposition and susceptibility to infectious agents.
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Affiliation(s)
- Perrine Hugon
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Jean-Charles Dufour
- Assistance Publique des Hôpitaux de Marseille, BioSTIC, Pôle de Santé Publique, Marseille, France; Aix-Marseille Université, UMR912 SESSTIM (AMU-INSERM-IRD), Marseille, France
| | - Philippe Colson
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Kankoe Sallah
- Aix-Marseille Université, UMR912 SESSTIM (AMU-INSERM-IRD), Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
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Bittar F, Bibi F, Ramasamy D, Lagier JC, Azhar EI, Jiman-Fatani AA, Al-Ghamdi AK, Nguyen TT, Yasir M, Fournier PE, Raoult D. Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov. Stand Genomic Sci 2015; 10:47. [PMID: 26380635 PMCID: PMC4572673 DOI: 10.1186/s40793-015-0024-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 05/21/2015] [Indexed: 11/13/2022] Open
Abstract
Strain JCE(T) was isolated from the fecal sample of a 24-year-old obese man living in Jeddah, Saudi Arabia. It is an aerobic, Gram-positive, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.5 % with Bacillus niacini, the phylogenetically closest species with standing nomenclature. Moreover, the strain JCE(T) presents many phenotypic differences, when it is compared to other Bacillus species, and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,762,944 bp long genome (1 chromosome but no plasmid) contains 4,654 protein-coding and 98 RNAs genes, including 92 tRNA genes. The strain JCE(T) differs from most of the other closely Bacillus species by more than 1 % in G + C content. In addition, digital DNA-DNA hybridization values for the genome of the strain JCE(T) against the closest Bacillus genomes range between 19.5 to 28.1, that confirming again its new species status. On the basis of these polyphasic data made of phenotypic and genomic analyses, we propose the creation of Bacillus jeddahensis sp. nov. that contains the strain JCE(T).
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Affiliation(s)
- Fadi Bittar
- />URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Fehmida Bibi
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Esam I. Azhar
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- />Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asif A. Jiman-Fatani
- />Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed K. Al-Ghamdi
- />Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ti Thien Nguyen
- />URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Muhammad Yasir
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Didier Raoult
- />URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
- />Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 2015; 28:237-64. [PMID: 25567229 DOI: 10.1128/cmr.00014-14] [Citation(s) in RCA: 507] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.
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Fournier PE, Drancourt M. New Microbes New Infections promotes modern prokaryotic taxonomy: a new section "TaxonoGenomics: new genomes of microorganisms in humans". New Microbes New Infect 2015. [PMID: 26199732 PMCID: PMC4506979 DOI: 10.1016/j.nmni.2015.06.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005, Marseille, France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005, Marseille, France
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Veloo A, Elgersma P, van Winkelhoff A. Anaerococcus degenerii sp. nov., isolated from human clinical specimens. Anaerobe 2015; 33:71-5. [DOI: 10.1016/j.anaerobe.2015.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 02/05/2015] [Accepted: 02/08/2015] [Indexed: 10/24/2022]
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Angelakis E, Bibi F, Ramasamy D, Azhar EI, Jiman-Fatani AA, Aboushoushah SM, Lagier JC, Robert C, Caputo A, Yasir M, Fournier PE, Raoult D. Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov. Stand Genomic Sci 2014; 9:8. [PMID: 25780501 PMCID: PMC4334108 DOI: 10.1186/1944-3277-9-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 12/03/2022] Open
Abstract
Clostridium saudii strain JCC(T) sp. nov. is the type strain of C. saudii sp. nov., a new species within the genus Clostridia. This strain, whose genome is described here, was isolated from a fecal sample collected from an obese 24-year-old (body mass index 52 kg/m2) man living in Jeddah, Saudi Arabia. C. saudii is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,653,762 bp long genome contains 3,452 protein-coding and 53 RNA genes, including 4 rRNA genes.
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Affiliation(s)
- Emmanouil Angelakis
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Dhamodharan Ramasamy
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asif A Jiman-Fatani
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sally M Aboushoushah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Aurelia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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Angelakis E, Raoult D. Methods for the discovery of emerging pathogens. Microb Pathog 2014; 77:114-8. [PMID: 25014736 PMCID: PMC7127287 DOI: 10.1016/j.micpath.2014.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 06/23/2014] [Indexed: 01/18/2023]
Abstract
Recently, there has been a steady increase in the number of recognized pathogenic microorganisms, specifically bacteria. The development of genetic technologies, MALDI-TOF mass spectrometry and new culturing techniques has significantly widened the repertoire of known microorganisms and therefore pathogenic microorganisms. The repertoire of infectious agents has been studied in various environments including water, soil, pets, livestock, wildlife and arthropods. Using different methods, many known pathogens can be identified in these samples; therefore, the impact of emergent pathogens on humans can be examined and novel pathogens can be identified. In this special issue, we discuss the identification of emerging pathogens in the environment and animals.
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Affiliation(s)
- Emmanouil Angelakis
- URMITE CNRS-IRD 198 UMR 6236, Université de la Méditerranée, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille, France.
| | - Didier Raoult
- URMITE CNRS-IRD 198 UMR 6236, Université de la Méditerranée, Faculté de Médecine, 27 Bd Jean Moulin, 13385 Marseille, France
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Pagnier I, Croce O, Robert C, Raoult D, La Scola B. Non-contiguous finished genome sequence and description of Anaerococcus provenciensis sp. nov. Stand Genomic Sci 2014; 9:1198-210. [PMID: 25197492 PMCID: PMC4149013 DOI: 10.4056/sigs.5501035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Anaerococcus provenciensis strain 9402080(T) sp. nov. is the type strain of A. provenciensis sp. nov., a new species within the genus Anaerococcus. This strain was isolated from a cervical abscess sample. A. provenciensis is a Gram-positive anaerobic cocci. Here, we describe the features of this organism, together with the complete genome sequence and annotation. The 2.26 Mbp long genome contains 2099 protein-coding and 57 RNA genes including 8 rRNA genes and exhibits a G+C content of 33.48%.
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Affiliation(s)
- Isabelle Pagnier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236 – IRD 198, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France
| | - Olivier Croce
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236 – IRD 198, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236 – IRD 198, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236 – IRD 198, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236 – IRD 198, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385 Marseille cedex 05, France
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Ikram HI, Catherine R, Caroline M, Didier R, Hocine H, Christelle D. Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov. Stand Genomic Sci 2014; 9:956-9. [PMID: 25197441 PMCID: PMC4149028 DOI: 10.4056/sigs.4618288] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Halopiger goleamassiliensis strain IIH3(T) sp. nov. is a novel, extremely halophilic archaeon within the genus Halopiger. This strain was isolated from an evaporitic sediment in El Golea Lake, Ghardaïa region (Algeria). The type strain is strain IIH3(T). H. goleamassiliensis is moderately thermophilic, neutrophilic, non-motile and coccus-shaped. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,906,923 bp long genome contains 3,854 protein-encoding genes and 49 RNA genes (1 gene is 16S rRNA, 1 gene is 23S rRNA, 3 genes are 5S rRNA, and 44 are tRNA genes).
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Affiliation(s)
- Hassani Imene Ikram
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
| | | | | | | | - Hacène Hocine
- USTHB Université, Laboratoire de Biologie Cellulaire et Moléculaire, Faculté de Biologie Algérie
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Padmanabhan R, Dubourg G, Nguyen TT, Couderc C, Rossi-Tamisier M, Caputo A, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Collinsella massiliensis sp. nov. Stand Genomic Sci 2014; 9:1144-58. [PMID: 25197489 PMCID: PMC4149003 DOI: 10.4056/sigs.5399696] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Collinsella massiliensis strain GD3(T) is the type strain of Collinsella massiliensis sp. nov., a new species within the genus Collinsella. This strain, whose genome is described here, was isolated from the fecal flora of a 53-year-old French Caucasoid woman who had been admitted to intensive care unit for Guillain-Barré syndrome. Collinsella massiliensis is a Gram-positive, obligate anaerobic, non motile and non sporulating bacillus. Here, we describe the features of this organism, together with the complete genome sequence and annotation. The genome is 2,319,586 bp long (1 chromosome, no plasmid), exhibits a G+C content of 65.8% and contains 2,003 protein-coding and 54 RNA genes, including 1 rRNA operon.
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Affiliation(s)
- Roshan Padmanabhan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Gregory Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Jean-Christophe lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Thi-Thien Nguyen
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Carine Couderc
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Morgane Rossi-Tamisier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Aurelia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille cedex 05, France
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Keita MB, Padhmananabhan R, Caputo A, Robert C, Delaporte E, Raoult D, Fournier PE, Bittar F. Non-contiguous finished genome sequence and description of Paenibacillus gorillae sp. nov. Stand Genomic Sci 2014; 9:1031-45. [PMID: 25197481 PMCID: PMC4149019 DOI: 10.4056/sigs.5189179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Strain G1(T) sp. nov. is the type strain of Paenibacillus gorillae a newly proposed species within the genus Paenibacillus. This strain, whose genome is described here, was isolated in France from the fecal sample of a wild western lowland gorilla from Cameroon. P. gorillae is a facultative anaerobic, Gram-negative, rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,257,967 bp long genome (one chromosome but no plasmid) contains 5,856 protein-coding and 62 RNAs genes, including 60 tRNA genes.
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Affiliation(s)
| | | | - Aurélia Caputo
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Catherine Robert
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
| | | | - Didier Raoult
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
- King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | | | - Fadi Bittar
- URMITE, Aix-Marseille Université, Faculté de médecine, Marseille, France
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Lagier JC, Bibi F, Ramasamy D, Azhar EI, Robert C, Yasir M, Jiman-Fatani AA, Alshali KZ, Fournier PE, Raoult D. Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov. Stand Genomic Sci 2014; 9:1003-19. [PMID: 25197479 PMCID: PMC4148971 DOI: 10.4056/sigs.5571026] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clostridium jeddahense strain JCD(T) (= CSUR P693 = DSM 27834) is the type strain of C. jeddahense sp. nov. This strain, whose genome is described here, was isolated from the fecal flora of an obese 24 year-old Saudian male (BMI=52 kg/m(2)). Clostridium jeddahense strain JCD(T) is an obligate Gram-positive bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,613,503 bp long genome (1 chromosome, no plasmid) exhibits a G+C content of 51.95% and contains 3,462 protein-coding and 53 RNA genes, including 4 rRNA genes.
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Affiliation(s)
- Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278 – IRD 198, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Dhamodharan Ramasamy
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278 – IRD 198, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - Esam I. Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278 – IRD 198, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Khalid Z. Alshali
- Department of Medicine, Faculty of Medicine, King Abdulaziz University, PO Box 80215, Jeddah, Postal code 21589, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278 – IRD 198, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278 – IRD 198, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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Pagnier I, Croce O, Robert C, Raoult D, La Scola B. Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium. Stand Genomic Sci 2014; 9:704-17. [PMID: 25197455 PMCID: PMC4148993 DOI: 10.4056/sigs.3957647] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Fenollaria massiliensis strain 9401234(T), is the type strain of Fenollaria massiliensis gen. nov., sp. nov., a new species within a new genus Fenollaria. This strain, whose genome is described here, was isolated from an osteoarticular sample. F. massiliensis strain 9401234(T) is an obligate anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1.71 Mbp long genome exhibits a G+C content of 34.46% and contains 1,667 protein-coding and 30 RNA genes, including 3 rRNA genes.
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Affiliation(s)
- Isabelle Pagnier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de médecine, Aix-Marseille Université, France
| | - Olivier Croce
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de médecine, Aix-Marseille Université, France
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de médecine, Aix-Marseille Université, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de médecine, Aix-Marseille Université, France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Faculté de médecine, Aix-Marseille Université, France
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Samb-Ba B, Mazenot C, Gassama-Sow A, Dubourg G, Richet H, Hugon P, Lagier JC, Raoult D, Fenollar F. MALDI-TOF identification of the human Gut microbiome in people with and without diarrhea in Senegal. PLoS One 2014; 9:e87419. [PMID: 24784934 PMCID: PMC4006720 DOI: 10.1371/journal.pone.0087419] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/24/2013] [Indexed: 12/21/2022] Open
Abstract
Background In Africa, there are several problems with the specific identification of bacteria. Recently, MALDI-TOF mass spectrometry has become a powerful tool for the routine microbial identification in many clinical laboratories. Methodology/Principal Findings This study was conducted using feces from 347 individuals (162 with diarrhea and 185 without diarrhea) sampled in health centers in Dakar, Senegal. Feces were transported from Dakar to Marseille, France, where they were cultured using different culture conditions. The isolated colonies were identified using MALDI-TOF. If a colony was unidentified, 16S rRNA sequencing was performed. Overall, 2,753 isolates were tested, allowing for the identification of 189 bacteria from 5 phyla, including 2 previously unknown species, 11 species not previously reported in the human gut, 10 species not previously reported in humans, and 3 fungi. 2,718 bacterial isolates (98.8%) out of 2,750 yielded an accurate identification using mass spectrometry, as did the 3 Candida albicans isolates. Thirty-two bacterial isolates not identified by MALDI-TOF (1.2%) were identified by sequencing, allowing for the identification of 2 new species. The number of bacterial species per fecal sample was significantly higher among patients without diarrhea (8.6±3) than in those with diarrhea (7.3±3.4; P = 0.0003). A modification of the gut microbiota was observed between the two groups. In individuals with diarrhea, major commensal bacterial species such as E. coli were significantly decreased (85% versus 64%), as were several Enterococcus spp. (E. faecium and E. casseliflavus) and anaerobes, such as Bacteroides spp. (B. uniformis and B. vulgatus) and Clostridium spp. (C. bifermentans, C. orbiscindens, C. perfringens, and C. symbosium). Conversely, several Bacillus spp. (B. licheniformis, B. mojavensis, and B. pumilus) were significantly more frequent among patients with diarrhea. Conclusions/Significance MALDI-TOF is a potentially powerful tool for routine bacterial identification in Africa, allowing for a quick identification of bacterial species.
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Affiliation(s)
- Bissoume Samb-Ba
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
- Unité de Bactériologie Expérimentale, Institut Pasteur de Dakar, Dakar, Senegal
| | - Catherine Mazenot
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Amy Gassama-Sow
- Unité de Bactériologie Expérimentale, Institut Pasteur de Dakar, Dakar, Senegal
| | - Grégory Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Hervé Richet
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Perrine Hugon
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
| | - Florence Fenollar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63, CNRS 7278, IRD 198, INSERM 1095, Aix-Marseille Université, Marseille, France and Dakar, Senegal
- * E-mail:
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Edouard S, Bibi F, Dhamodharan R, Lagier JC, Azhar EI, Robert C, Caputo A, Yasir M, Jiman-Fatani AA, Alawi M, Fournier PE, Raoult D. Non-contiguous finished genome sequence and description of Corynebacterium jeddahense sp. nov. Stand Genomic Sci 2014; 9:987-1002. [PMID: 25197478 PMCID: PMC4149016 DOI: 10.4056/sigs.5561028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Corynebacterium jeddahense sp. nov., strain JCBT, is the type strain of Corynebacterium jeddahense sp. nov., a new species within the genus Corynebacterium. This strain, whose genome is described here, was isolated from fecal flora of a 24-year-old Saudi male suffering from morbid obesity. Corynebacterium jeddahense is a Gram-positive, facultative anaerobic, nonsporulating bacillus. Here, we describe the features of this bacterium, together with the complete genome sequencing and annotation, and compare it to other member of the genus Corynebacterium. The 2,472,125 bp-long genome (1 chromosome but not plasmid) contains 2,359 protein-coding and 53 RNA genes, including 1 rRNA operon.
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Affiliation(s)
- Sophie Edouard
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Ramasamy Dhamodharan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France
| | - Esam Ibraheen Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia . ; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France
| | - Aurelia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Asif Ahmad Jiman-Fatani
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maha Alawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia ; Infection Control Unit, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Boulevard Jean Moulin, Marseille cedex, France ; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
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Cassir N, Croce O, Pagnier I, Benamar S, Couderc C, Robert C, Raoult D, La Scola B. Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium. Stand Genomic Sci 2014; 9:794-806. [PMID: 25197464 PMCID: PMC4149005 DOI: 10.4056/sigs.5159098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteroides neonati strain MS4(T), is the type strain of Bacteroides neonati sp. nov., a new species within the genus Bacteroides. This strain, whose genome is described here, was isolated from a premature neonate stool sample. B. neonati strain MS4(T) is an obligate anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5.03 Mbp long genome exhibits a G+C content of 43.53% and contains 4,415 protein-coding and 91 RNA genes, including 9 rRNA genes.
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Affiliation(s)
- Nadim Cassir
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France
| | - Olivier Croce
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France
| | - Isabelle Pagnier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France
| | - Samia Benamar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France
| | - Carine Couderc
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), Facultés de Médecine et de Pharmacie, Aix-Marseille Université, France
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50
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Edouard S, Sankar S, Dangui NPM, Lagier JC, Michelle C, Raoult D, Fournier PE. Genome sequence and description of Nesterenkonia massiliensis sp. nov. strain NP1(T.). Stand Genomic Sci 2014; 9:866-82. [PMID: 25197469 PMCID: PMC4148991 DOI: 10.4056/sigs.5631022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Nesterenkonia massiliensis sp. nov., strain NP1T, is the type strain of Nesterenkonia massiliensis sp. nov., a new species within the genus Nesterenkonia. This strain, whose genome is described here, was isolated from the feces of a 32-year-old French woman suffering from AIDS and living in Marseille. Nesterenkonia massiliensis is a Gram-positive aerobic coccus. Here, we describe the features of this bacterium, together with the complete genome sequencing and annotation. The 2,726,371 bp long genome (one chromosome but no plasmid) contains 2,663 protein-coding and 51 RNA genes, including 1 rRNA operon.
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Affiliation(s)
- Sophie Edouard
- Aix-Marseille Université, Faculté de médecine, Marseille, France
| | - Senthil Sankar
- Aix-Marseille Université, Faculté de médecine, Marseille, France
| | | | | | | | - Didier Raoult
- Aix-Marseille Université, Faculté de médecine, Marseille, France . ; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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