51
|
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%.
Collapse
|
52
|
Tran TLQ, Anani H, Trinh HT, Pham TPT, Dang VK, Ho VM, Bui NHL, Nguyen NH, Raoult D, Trinh TT, Fournier PE. Chitinophaga vietnamensis sp. nov. , a multi-drug resistant bacterium infecting humans. Int J Syst Evol Microbiol 2020; 70:1758-1768. [PMID: 32228771 DOI: 10.1099/ijsem.0.003968] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe a new multidrug resistant Chitinophaga species that was isolated from patients with type 2 diabetes in Vietnam. Strain BD 01T was cultivated in 2017 from a blood sample of a patient suffering from bacteremia. Strain VP 7442 was isolated in 2018 from a pleural fluid sample of a patient who had presented with lung abscess and pleural effusion. Both strains are aerobic, Gram-negative, non-motile and non-spore-forming. The 16S rRNA gene sequences of both strains are 100 % similar and share a highest 16S sequence identity with Chitinophaga polysaccharea MRP-15T of 97.42 %. Their predominant fatty acid is iso-C15 : 0 (73.8 % for strain BD 01T and 79.8 % for strain VP 7442). The draft genome sizes of strains BD 01T and VP 7442 are 6 308 408 and 6 308 579 bp, respectively. They are resistant to beta-lactams, aminoglycosides, fluoroquinolones, metronidazole, fosfomycin, vancomycin and macrolides, and exhibit 20 and 18 antimicrobial resistance-related genes, respectively. Using the multiphasic taxonogenomic approach, we propose that strains BD 01T (=CSUR P9622=VTCC 70981) and VP 7442 (=CSUR P9623=VTCC 70982) represent a new species, for which we propose the name Chitinophaga vietnamensis sp. nov. Strain BD 01T was chosen as type strain of C. vietnamensis sp. nov.
Collapse
Affiliation(s)
- Thi Le Quyen Tran
- Institute of Microbiology and Biotechnology (IMBT), Vietnam National University, Hanoi, Vietnam
| | - Hussein Anani
- IHU Méditerranée Infection, Marseille, France.,Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France
| | - Ho Tinh Trinh
- Binh Dinh General Hospital, Binh Dinh Province, Vietnam
| | - Thi Phuong Thao Pham
- Institute of Microbiology and Biotechnology (IMBT), Vietnam National University, Hanoi, Vietnam
| | | | - Viet My Ho
- Binh Dinh General Hospital, Binh Dinh Province, Vietnam
| | - Nguyen Hai Linh Bui
- Institute of Microbiology and Biotechnology (IMBT), Vietnam National University, Hanoi, Vietnam
| | | | - Didier Raoult
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| | - Thanh Trung Trinh
- Institute of Microbiology and Biotechnology (IMBT), Vietnam National University, Hanoi, Vietnam
| | - Pierre Edouard Fournier
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France.,IHU Méditerranée Infection, Marseille, France
| |
Collapse
|
53
|
Kangale LJ, Raoult D, Ghigo E, Fournier PE. Pedobacter schmidteae sp. nov., a new bacterium isolated from the microbiota of the planarian Schmidtea mediterranea. Sci Rep 2020; 10:6113. [PMID: 32273530 PMCID: PMC7145819 DOI: 10.1038/s41598-020-62985-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 03/17/2020] [Indexed: 12/22/2022] Open
Abstract
Pedobacter schmidteae sp. nov. strain EGT (Collection de Souches de l'Unité des Rickettsie CSUR P6417 = Colección Española de Cultivos Tipo CECT 9771) is a new Pedobacter species isolated from the planarian Schmidtea mediterranea. Schmidtea mediterranea are flatworms living in freshwater and exhibiting an unusual ability to regenerate amputated parts. To date, the gut microbiota of Schmidtea mediterranea remains poorly studied. Here, via the culturomics strategy that consists in using diversified culture conditions, we isolated a new bacterium, strain EG, that we characterized using the taxono-genomics approach that combines phenotypic assays and genome sequencing and analysis. Strain EG exhibits a 16S rRNA sequence similarity of 98.29% with Pedobacter nyackensis strain NWG-II14T, its closest neighbour with standing in nomenclature. It is an aerobic bacterium belonging to the family Sphingobacteriaceae. Colonies are small, round, smooth and transparent. Bacterial cells are Gram-negative, rod-shaped, motile and non-spore-forming bacilli with positive catalase and oxidase activities. The genome sequence is 6,198,518 bp-long with a G + C content of 41.13%, and the Ortho-ANI and dDDH values when compared to P. nyackensis are 77.34% and 21.50%, respectively. Strain EGT exhibits unique characteristics that classify it as the type strain of new bacterial species for which we propose the name Pedobacter schmidteae sp. nov.
Collapse
Affiliation(s)
- Luis Johnson Kangale
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
- IHU-Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée-Infection, Marseille, France
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- TechnoJouvence, 19-21 Boulevard Jean Moulin 13385, Marseille, cedex, 05, France
| | - Eric Ghigo
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
- IHU-Méditerranée-Infection, Marseille, France.
- TechnoJouvence, 19-21 Boulevard Jean Moulin 13385, Marseille, cedex, 05, France.
| | - Pierre-Edouard Fournier
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
- IHU-Méditerranée-Infection, Marseille, France.
- TechnoJouvence, 19-21 Boulevard Jean Moulin 13385, Marseille, cedex, 05, France.
| |
Collapse
|
54
|
Liu R, Gu Y, Shen M, Li H, Zhang K, Wang Q, Wei X, Zhang H, Wu D, Yu K, Cai W, Wang G, Zhang S, Sun Q, Huang P, Wang Z. Predicting postmortem interval based on microbial community sequences and machine learning algorithms. Environ Microbiol 2020; 22:2273-2291. [PMID: 32227435 DOI: 10.1111/1462-2920.15000] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/18/2020] [Accepted: 03/22/2020] [Indexed: 11/29/2022]
Abstract
Microbes play an essential role in the decomposition process but were poorly understood in their succession and behaviour. Previous researches have shown that microbes show predictable behaviour that starts at death and changes during the decomposition process. Research of such behaviour enhances the understanding of decomposition and benefits estimating the postmortem interval (PMI) in forensic investigations, which is critical but faces multiple challenges. In this study, we combined microbial community characterization, microbiome sequencing from different organs (i.e. brain, heart and cecum) and machine learning algorithms [random forest (RF), support vector machine (SVM) and artificial neural network (ANN)] to investigate microbial succession pattern during corpse decomposition and estimate PMI in a mouse corpse system. Microbial communities exhibited significant differences between the death point and advanced decay stages. Enterococcus faecalis, Anaerosalibacter bizertensis, Lactobacillus reuteri, and so forth were identified as the most informative species in the decomposition process. Furthermore, the ANN model combined with the postmortem microbial data set from the cecum, which was the best combination among all candidates, yielded a mean absolute error of 1.5 ± 0.8 h within 24-h decomposition and 14.5 ± 4.4 h within 15-day decomposition. This integrated model can serve as a reliable and accurate technology in PMI estimation.
Collapse
Affiliation(s)
- Ruina Liu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yuexi Gu
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Mingwang Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Huan Li
- Department of Microbiology and immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Kai Zhang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qi Wang
- Chongqing Medical University, College of Basic Medicine, Department of Forensic Medicine, Chongqing, 400016, China
| | - Xin Wei
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Haohui Zhang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Di Wu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Kai Yu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Wumin Cai
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Gongji Wang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Siruo Zhang
- Department of Microbiology and immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Qinru Sun
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Ping Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Zhenyuan Wang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| |
Collapse
|
55
|
Ngom I, Hasni I, Lo C, Traore S, Fontanini A, Raoult D, Fenollar F. Taxono-genomics and description of Gordonibacter massiliensis sp. nov., a new bacterium isolated from stool of healthy patient. New Microbes New Infect 2020; 33:100624. [PMID: 31890230 PMCID: PMC6931061 DOI: 10.1016/j.nmni.2019.100624] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 11/14/2019] [Indexed: 12/22/2022] Open
Abstract
Using the taxono-genomics concept, we describe here a strictly anaerobic Gram-positive bacillus. This strain was isolated from the stool sample of a 50-year-old healthy Bedouin woman. The 16S rRNA gene sequence analysis and the whole-genome sequencing showed that this isolate belonged to the genus Gordonibacter in the family Eggerthellaceae. Based on these criteria, we propose the creation of Gordonibacter massiliensis sp. nov., strain Marseille-P2775T (= CSUR P2775).
Collapse
Affiliation(s)
- I.I. Ngom
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - I. Hasni
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - S.I. Traore
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - A. Fontanini
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| |
Collapse
|
56
|
Abou Abdallah R, Okdah L, Bou Khalil J, Anani H, Fournier PE, Raoult D, Bittar F. Draft genome and description of Chryseobacterium phocaeense sp. nov.: a new bacterial species isolated from the sputum of a cystic fibrosis patient. Arch Microbiol 2019; 201:1361-1368. [DOI: 10.1007/s00203-019-01704-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/21/2019] [Accepted: 07/10/2019] [Indexed: 11/28/2022]
|
57
|
Anani H, Abdallah RA, Khoder M, Fontanini A, Mailhe M, Ricaboni D, Raoult D, Fournier PE. Colibacter massiliensis gen. nov. sp. nov., a novel Gram-stain-positive anaerobic diplococcal bacterium, isolated from the human left colon. Sci Rep 2019; 9:17199. [PMID: 31748674 PMCID: PMC6868274 DOI: 10.1038/s41598-019-53791-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
The gut microbiota is considered to play a key role in human health. As a consequence, deciphering its microbial diversity is mandatory. A polyphasic taxonogenomic strategy based on the combination of phenotypic and genomic analyses was used to characterize a new bacterium, strain Marseille-P2911. This strain was isolated from a left colon sample of a 60-year old man who underwent a colonoscopy for an etiological investigation of iron-deficiency anemia in Marseille, France. On the basis of 16S rRNA sequence comparison, the closest phylogenetic neighbor was Anaeroglobus geminatus (94.59% 16S rRNA gene sequence similarity) within the family Veillonellaceae. Cells were anaerobic, Gram-stain-positive, non-spore-forming, catalase/oxidase negative cocci grouped in pairs. The bacterium was able to grow at 37 °C after 2 days of incubation. Strain Marseille-P2911 exhibited a genome size of 1,715,864-bp with a 50.2% G + C content, and digital DNA-DNA hybridization (dDDH) and OrthoANI values with A. geminatus of only 19.1 ± 4.5% and 74.42%, respectively. The latter value being lower than the threshold for genus delineation (80.5%), we propose the creation of the new genus Colibacter gen. nov., with strain Marseille-P2911T (=DSM 103304 = CSUR P2911) being the type strain of the new species Colibacter massiliensis gen. nov., sp. nov.
Collapse
Affiliation(s)
- Hussein Anani
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Rita Abou Abdallah
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - May Khoder
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Fontanini
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Morgane Mailhe
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Davide Ricaboni
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditeranéennes (VITROME), Marseille, France. .,Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.
| |
Collapse
|
58
|
Bellali S, Lo C, Naud S, Fonkou M, Armstrong N, Raoult D, Fournier PE, Fenollar F. Parabacteroides massiliensis sp. nov., a new bacterium isolated from a fresh human stool specimen. New Microbes New Infect 2019; 32:100602. [PMID: 31641517 PMCID: PMC6796604 DOI: 10.1016/j.nmni.2019.100602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/30/2019] [Indexed: 12/22/2022] Open
Abstract
Parabacteroides massiliensis sp. nov., strain Marseille-P2231T (= CSURP2231 = DSM 101860) is a new species within the family Tannerellaceae. It was isolated from a stool specimen of a 25-year-old healthy woman. Its genome was 5 013 798 bp long with a 45.7 mol% G+C content. The closest species based on 16S rRNA sequence was Parabacteroides merdae strain JCM 9497T with 98.19% sequence similarity. Considering phenotypic features and comparative genome studies, we proposed the strain Marseille-P2231T as the type strain of Parabacteroides massiliensis sp. nov., a new species within the genus Parabacteroides.
Collapse
Affiliation(s)
- S. Bellali
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - C.I. Lo
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - S. Naud
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - M.D.M. Fonkou
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - N. Armstrong
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
- IHU-Méditerranée Infection, Marseille, France
| | - P.-E. Fournier
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - F. Fenollar
- IHU-Méditerranée Infection, Marseille, France
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France
| |
Collapse
|
59
|
Traore SI, Bilen M, Beye M, Diop A, Mbogning Fonkou MD, Tall ML, Michelle C, Yasir M, Ibraheem Azhar E, Bibi F, Bittar F, Jiman‐Fatani AA, Daoud Z, Cadoret F, Fournier P, Edouard S. Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut. Microbiologyopen 2019; 8:e00758. [PMID: 30701700 PMCID: PMC6562231 DOI: 10.1002/mbo3.758] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 12/19/2022] Open
Abstract
As part of the culturomics project aiming at describing the human microbiota, we report in this study the description of the new bacterial genus Raoultibacter gen. nov. that includes two new species, that is, R. massiliensis sp. nov. and R. timonensis sp. nov. The R. massiliensis type strain Marseille-P2849T was isolated from the fecal specimen of a healthy 19-year-old Saudi Bedouin, while R. timonensis type strain Marseille-P3277T was isolated from the feces of an 11-year-old pygmy female living in Congo. Strain Marseille-P2849T exhibited 91.4% 16S rRNA sequence similarity with Gordonibacter urolithinfaciens, its phylogenetic closest neighbor with standing in nomenclature. As well, strain Marseille-P3277T exhibited 97.96% 16S rRNA similarity with strain Marseille-P2849T . Both strains were Gram-positive, motile, nonspore-forming rod and form transparent microcolonies on blood agar in both anaerobic and microaerophilic atmospheres. The genome sizes of strain Marseille-P2849T and strain Marseille-P3277T were 3,657,161 bp and 4,000,215 bp, respectively. Using a taxono-genomic approach combining the phenotypic, biochemical, and genomic characteristics, we propose the genus Raoultibacter gen. nov., which contains strains Marseille-P2849T (= CSUR P2849T , = DSM 103407T ) and Marseille-P3277T (=CCUG 70680T , =CSUR P3277T ) as type strains of the species R. massiliensis sp. nov., and R. timonensis sp. nov., respectively.
Collapse
Affiliation(s)
- Sory Ibrahima Traore
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Melhem Bilen
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
- Clinical Microbiology Department, Faculty of Medicine and Medical sciencesUniversity of BalamandAmiounLebanon
| | - Mamadou Beye
- UMR VITROME, IRD, AP‐HM, SSA, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Awa Diop
- UMR VITROME, IRD, AP‐HM, SSA, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | | | - Mamadou Lamine Tall
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Caroline Michelle
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia
- Medical Laboratory Technology Department, Faculty of Applied Medical SciencesKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research CenterKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Fadi Bittar
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Asif Ahmad Jiman‐Fatani
- Department of Medical Microbiology and Parasitology, Faculty of MedicineKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Ziad Daoud
- Department of Medical Microbiology and Parasitology, Faculty of MedicineKing Abdulaziz UniversityJeddahSaudi Arabia
| | - Fréderic Cadoret
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Pierre‐Edouard Fournier
- UMR VITROME, IRD, AP‐HM, SSA, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| | - Sophie Edouard
- UMR MEPHI, IRD, APHM, IHU Méditerranée‐InfectionAix‐Marseille UniversitéMarseilleFrance
| |
Collapse
|
60
|
Anani H, Abou Abdallah R, Chelkha N, Fontanini A, Ricaboni D, Mailhe M, Raoult D, Fournier PE. Draft genome and description of Merdibacter massiliensis gen.nov., sp. nov., a new bacterium genus isolated from the human ileum. Sci Rep 2019; 9:7931. [PMID: 31138831 PMCID: PMC6538751 DOI: 10.1038/s41598-019-44343-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/09/2019] [Indexed: 12/22/2022] Open
Abstract
We used phenotypic, genomic and phylogenetic information following the taxono-genomics approach to demonstrate that strain Marseille–P3254, isolated from an ileal sample of a 76-year old woman who underwent upper and lower digestive tract endoscopy for esophagitis and colonic polyp, is representative of a novel bacterial genus within the family Erysipelotrichaceae in the phylum Firmicutes. It is an anaerobic Gram-negative bacterium without catalase and oxidase activities. The genome of strain Marseille–P3254 is 2,468,496-bp long with a 40.1% G + C content. This new bacterium is most closely related to Eubacterium dolichum, with which it shares 90.7% 16S rRNA sequence similarity. In addition, genomic comparison using the digital DNA–DNA hybridization and OrthoANI analyses between the novel organism and the E. dolichum type strain revealed identities of 25.2 and 68.91%, respectively. The major fatty acids were C16: 0, C18: 1n9 and C18: 0. Based on these data, we propose the creation of the new genus Merdibacter gen. nov., with strain Marseille-P3254T (=CSUR P3254 = DSM 103534) being the type strain of the new species Merdibacter massiliensis gen. nov., sp. nov.
Collapse
Affiliation(s)
- Hussein Anani
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Rita Abou Abdallah
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nisrine Chelkha
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Anthony Fontanini
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Davide Ricaboni
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Morgane Mailhe
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, AP-HM, UMR Vecteurs Infections Tropicales et Méditerranéennes (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.
| |
Collapse
|
61
|
Bonnet M, Mailhe M, Ricaboni D, Labas N, Richez M, Vitton V, Benezech A, Fournier PE, Million M, Raoult D, Khelaifia S. Genome sequence and description of Traorella massiliensis gen. nov., sp. nov., a new bacterial genus isolated from human left colon. New Microbes New Infect 2019; 29:100520. [PMID: 30949346 PMCID: PMC6428956 DOI: 10.1016/j.nmni.2019.100520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/07/2019] [Accepted: 02/13/2019] [Indexed: 12/22/2022] Open
Abstract
A strictly anaerobic, motile, non-spore-forming, Gram-negative, rod-shaped bacterium designated Marseille-P3110T was isolated from the left colon cleansing of a 76-year-old Frenchwoman. Its 16S ribosomal RNA (rRNA) gene showed a 93.2% similarity level with the 16S rRNA of Dielma fastidiosa strain JC13, the closest species with a validly published name. The genome of Marseille-P3110T is 2 607 061 bp long with 35.99% G+C content. Of the 2642 predicted genes, 2582 were protein-coding genes and 60 were RNAs, including five 16S rRNA genes.
Collapse
Affiliation(s)
- M. Bonnet
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - M. Mailhe
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - D. Ricaboni
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
- Département des sciences cliniques et biomédicales, Luigi Sacco, Division des Maladies Infectieuses III, Université de Milan, Milan, Italy
| | - N. Labas
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - M. Richez
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - 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
| | - P.-E. Fournier
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Service de Gastroentérologie, Hopital Nord, Assistance Publique-Hopitaux de Marseille, Marseille, France
- Département des sciences cliniques et biomédicales, Luigi Sacco, Division des Maladies Infectieuses III, Université de Milan, Milan, Italy
| | - M. Million
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - S. Khelaifia
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| |
Collapse
|
62
|
Dubourg G, Baron S, Cadoret F, Couderc C, Fournier PE, Lagier JC, Raoult D. From Culturomics to Clinical Microbiology and Forward. Emerg Infect Dis 2019; 24:1683-1690. [PMID: 30124405 PMCID: PMC6106433 DOI: 10.3201/eid2409.170995] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Culturomics has permitted discovery of hundreds of new bacterial species isolated from the human microbiome. Profiles generated by using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry have been added to the mass spectrometer database used in clinical microbiology laboratories. We retrospectively collected raw data from MALDI-TOF mass spectrometry used routinely in our laboratory in Marseille, France, during January 2012-March 2018 and analyzed 16S rDNA sequencing results from misidentified strains. During the study period, 744 species were identified from clinical specimens, of which 21 were species first isolated from culturomics. This collection involved 105 clinical specimens, accounting for 98 patients. In 64 cases, isolation of the bacteria was considered clinically relevant. MALDI-TOF mass spectrometry was able to identify the species in 95.2% of the 105 specimens. While contributing to the extension of the bacterial repertoire associated with humans, culturomics studies also enlarge the spectrum of prokaryotes involved in infectious diseases.
Collapse
|
63
|
Nicaise B, Maaloum M, Lo CI, Armstrong N, Bretelle F, Fournier PÉ, Diop K, Fenollar F. Taxono-genomics description of 'Lactobacillus raoultii sp. nov.', strain Marseille-P4006 T, a new Lactobacillus species isolated from the female genital tract of a patient with bacterial vaginosis. New Microbes New Infect 2019; 29:100534. [PMID: 31011428 PMCID: PMC6462780 DOI: 10.1016/j.nmni.2019.100534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 03/14/2019] [Indexed: 12/31/2022] Open
Abstract
Strain Marseille-P4006T, a Gram-stain-positive, rod-shaped, non-sporulating, facultatively anaerobic bacterium, was isolated from the vaginal swab of a 45-year-old woman with recurrent bacterial vaginosis. We studied its phenotypic characteristics and sequenced its whole genome. The major fatty acids were C16:0 (48%), C19:1n9 (14%) and C18:0 (11%). The 3 070 142-bp-long genome contains 2855 protein-coding genes and 68 RNAs. Strain Marseille-P4006T exhibited 98.1% 16S rRNA similarity with Lactobacillus farraginis, the closest species phylogenetically. Thus, strain Marseille-P4006 is distinct enough to represent a new species for which we propose the name Lactobacillus raoultii sp. nov. The type strain is Marseille-P4006T.
Collapse
Affiliation(s)
- B Nicaise
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - M Maaloum
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France.,Faculty of Sciences Ben M'Sik, Laboratory of Biology and Health, Hassan II University, Casablanca, Morocco
| | - C I Lo
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - N Armstrong
- IHU-Méditerranée Infection, Marseille, France.,Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France
| | - F Bretelle
- IHU-Méditerranée Infection, Marseille, France.,Aix-Marseille University, IRD, AP-HM, MEPHI, Marseille, France.,Department of Gynaecology and Obstetrics, Gynépole, Hôpital Nord, AP-HM, Marseille, France
| | - P-É Fournier
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - K Diop
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - F Fenollar
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| |
Collapse
|
64
|
Mbogning Fonkou MD, Bilen M, Gouba N, Khelaifia S, Cadoret F, Nguyen TT, Richez M, Bittar F, Fournier PE, Raoult D, Dubourg G. Non-contiguous finished genome sequencing and description of Enterococcus timonensis sp. nov. isolated from human sputum. New Microbes New Infect 2019; 29:100532. [PMID: 31011427 PMCID: PMC6461582 DOI: 10.1016/j.nmni.2019.100532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/14/2019] [Indexed: 12/22/2022] Open
Abstract
Enterococcus timonensis sp. nov., strain Marseille-P2817T, is a facultatively anaerobic, motile and non-spore-forming Gram-positive coccus which was isolated from the sputum of a healthy adult man in Marseilles. We present herein its phenotypic description together with MALDI-TOF (matrix-assisted laser-desorption/ionization time-of-flight) mass spectrometry analysis and genome sequencing and comparison. The genome of Enterococcus timonensis is 2 123 933 bp long with 38.46 mol% of G+C content, and it contains 1983 protein-coding genes and 65 RNA genes (including nine rRNA genes).
Collapse
Affiliation(s)
- M D Mbogning Fonkou
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - M Bilen
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - N Gouba
- Institut Supérieur des Sciences de La Santé (INSSA), Université Polytechnique de Bobo Dioulasso, Burkina Faso
| | - S Khelaifia
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - F Cadoret
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - T T Nguyen
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - M Richez
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - F Bittar
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| | - P-E Fournier
- Aix Marseille Univ, IRD, VITROME, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - D Raoult
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - G Dubourg
- MEPHI, UMR, IRD, Aix-Marseille Univ, Marseille, France, Facultés de Médecine et de Pharmacie, Marseille, France
| |
Collapse
|
65
|
Hosny M, Abdallah RA, Bou Khalil J, Fontanini A, Baptiste E, Armstrong N, La Scola B. Clostridium pacaense: a new species within the genus Clostridium. New Microbes New Infect 2019; 28:6-10. [PMID: 30740227 PMCID: PMC6357548 DOI: 10.1016/j.nmni.2018.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 11/29/2022] Open
Abstract
Using the strategy of taxonogenomics, we described Clostridium pacaense sp. nov. strain Marseille-P3100T, a Gram-variable, nonmotile, spore-forming anaerobic bacillus. This strain was isolated from a 3.3-month-old Senegalese girl with clinical aspects of marasmus. The closest species based on 16S ribosomal RNA was Clostridium aldenense, with a similarity of 98.4%. The genome length was 2 672 129 bp, with a 50% GC content; 2360 proteins were predicted. Finally, predominant fatty acids were hexadecanoic acid, tetradecanoic acid and 9-hexadecenoic acid.
Collapse
Affiliation(s)
- M. Hosny
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - R. Abou Abdallah
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Vecteurs—Infections Tropicales et Méditerrannéennes (VITROME), Service de Santé des Armées, IHU-Méditerranée Infection, Marseille, France
| | - J. Bou Khalil
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - A. Fontanini
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - E. Baptiste
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - N. Armstrong
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - B. La Scola
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Marseille, France
| |
Collapse
|
66
|
Diop A, Diop K, Tomei E, Armstrong N, Bretelle F, Raoult D, Fenollar F, Fournier PE. Collinsella vaginalis sp. nov. strain Marseille-P2666 T, a new member of the Collinsella genus isolated from the genital tract of a patient suffering from bacterial vaginosis. Int J Syst Evol Microbiol 2019; 69:949-956. [PMID: 30806613 DOI: 10.1099/ijsem.0.003221] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A strictly anaerobic, Gram-stain-positive, non motile and non-spore-forming rod-shaped bacterium, strain Marseille-P2666T, was isolated using the culturomics approach from a vaginal sample of a French patient suffering from bacterial vaginosis. Cells were saccharolytic and were negative for catalase, oxidase, urease, nitrate reduction, indole production, hydrolysis of aesculin and gelatin. Strain Marseille-P2666T exhibited 97.04 % 16S rRNA sequence similarity to Collinsella tanakaei type strain YIT 12063T, the phylogenetically closest species with standing in nomenclature. The major fatty acids were C18:1ω9 (38 %), C16 : 0 (24 %) and C18 : 0 (19 %). The G+C content of the genome sequence of strain Marseille-P2666T is 64.6 mol%. On the basis of its phenotypic, phylogenetic and genomic features, strain Marseille-P2666T (=CSUR 2666T=DSM103342T) was classified as type strain of a novel species within the genus Collinsella for which the name Collinsella vaginalis sp. nov. is proposed.
Collapse
Affiliation(s)
- Awa Diop
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Khoudia Diop
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Enora Tomei
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Nicholas Armstrong
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Florence Bretelle
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France.,Department of Gynecology and Obstetrics, Gynépole, Marseille, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Didier Raoult
- UMR MEPHI, Aix-Marseille University, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Uuniversitaire Méditerranée Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Florence Fenollar
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| | - Pierre-Edouard Fournier
- UMR VITROME, Aix-Marseille Université, IRD, Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, Institut hospitalo-universitaire Méditerranée infection, Marseille, France
| |
Collapse
|
67
|
Description of Janibacter massiliensis sp. nov., cultured from the vaginal discharge of a patient with bacterial vaginosis. Antonie van Leeuwenhoek 2019; 112:1147-1159. [PMID: 30798490 DOI: 10.1007/s10482-019-01247-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/15/2019] [Indexed: 01/22/2023]
Abstract
Strain Marseille-P4121T was isolated from a vaginal sample of a 45-year-old French woman with bacterial vaginosis. It is a Gram-positive, asporogenous, non-motile and aerobic bacterium. Strain Marseille-P4121T exhibits 98.2% 16S rRNA sequence similarity with Janibacter alkaliphilus strain SCSIO 10480T, a phylogenetically closely related species with standing in nomenclature. Its major fatty acids were identified as C18:1ω9 (34.4%), C16:0 (30.1%), and C18:0 (19%). The draft genome size of strain Marseille-P4121T is 2,452,608 bp long with a 72.5% G+C content and contains 2351 protein-coding genes and 49 RNA genes including 3 rRNA genes. We propose that strain Marseille-P4121T (= CECT 9671T = CSUR P4121T) is the type strain of the new species Janibacter massiliensis sp. nov.
Collapse
|
68
|
Description and genomic characterization of Massiliimalia massiliensis gen. nov., sp. nov., and Massiliimalia timonensis gen. nov., sp. nov., two new members of the family Ruminococcaceae isolated from the human gut. Antonie van Leeuwenhoek 2019; 112:905-918. [DOI: 10.1007/s10482-018-01223-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/29/2018] [Indexed: 12/16/2022]
|
69
|
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]
|
70
|
Senghor B, Bassène H, Khelaifia S, Robert C, Fournier PE, Ruimy R, Sokhna C, Raoult D, Lagier JC. Oceanobacillus timonensis sp. nov. and Oceanobacillus senegalensis sp. nov., two new moderately halophilic, Gram-stain positive bacteria isolated from stools sample of healthy young Senegalese. Antonie van Leeuwenhoek 2018; 112:785-796. [DOI: 10.1007/s10482-018-01212-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 12/04/2018] [Indexed: 12/22/2022]
|
71
|
Ndongo S, Beye M, Dubourg G, Nguyen T, Couderc C, Fabrizio D, Fournier PE, Raoult D, Angelakis E. Genome analysis and description of Xanthomonas massiliensis sp. nov., a new species isolated from human faeces. New Microbes New Infect 2018; 26:63-72. [PMID: 30258635 PMCID: PMC6154774 DOI: 10.1016/j.nmni.2018.06.005] [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: 04/12/2018] [Revised: 06/08/2018] [Accepted: 06/13/2018] [Indexed: 12/22/2022] Open
Abstract
Xanthomonas massiliensis strain SN6T is a Gram-negative bacterium which is aerobic, motile and nonsporulating. This new species isolated from human faeces exhibited the characteristic traits of members of this genus, such as yellow pigmentation and viscosity. Here we present the main phenotypic characteristics and the taxonogenomics description of this strain. The genome is 3 690 720 bp long with DNA G + C content of about 70.52%.
Collapse
Affiliation(s)
- S. Ndongo
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - M. Beye
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - G. Dubourg
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - T.T. Nguyen
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - C. Couderc
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - D.P. Fabrizio
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - P.-E. Fournier
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - E. Angelakis
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
- Laboratory of Medical Microbiology, Hellenic Pasteur Institute, Athens, Greece
| |
Collapse
|
72
|
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.
Collapse
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
| |
Collapse
|
73
|
Andrieu C, Mailhe M, Ricaboni D, Fonkou MDM, Bilen M, Cadoret F, Tomei E, Armstrong N, Vitton V, Benezech A, Davoust B, Levasseur A, Lagier JC, Fournier PE, Raoult D. Noncontiguous finished genome sequences and description of Bacteroides mediterraneensis sp. nov., Bacteroides ihuae sp. nov., Bacteroides togonis sp. nov., Bacteroides ndongoniae sp. nov., Bacteroides ilei sp. nov. and Bacteroides congonensis sp. nov. identified by culturomics. New Microbes New Infect 2018; 26:73-88. [PMID: 30258636 PMCID: PMC6154776 DOI: 10.1016/j.nmni.2018.06.006] [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: 04/20/2018] [Revised: 06/08/2018] [Accepted: 06/13/2018] [Indexed: 12/22/2022] Open
Abstract
Culturomics is a concept developing different culture conditions in order to enlarge our knowledge of the human microbiota through the discovery of previously uncultured bacteria. This enabled us to isolate six new species of the Bacteroides genus: Bacteroides mediterraneensis strain Marseille-P2644, Bacteroides ihuae strain Marseille-P2824, Bacteroides togonis strain Marseille-P3166, Bacteroides ndongoniae strain Marseille-P3108, Bacteroides ilei strain Marseille-P3208 and Bacteroides congonensis strain Marseille-P3132. Those bacteria are Gram-negative anaerobic bacilli. We describe here their phenotypic features, together with phylogenetic analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry spectrum, fatty acid composition, and genome sequencing and annotation.
Collapse
Affiliation(s)
- C Andrieu
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - M Mailhe
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - D Ricaboni
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Département des Sciences Cliniques et Biomédicales, Luigi Sacco, Division des Maladies Infectieuses III, Université de Milan, Milan, Italy
| | - M D M Fonkou
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - M Bilen
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - F Cadoret
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - E Tomei
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - N Armstrong
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - 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
| | - B Davoust
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - A Levasseur
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - J-C Lagier
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - P-E Fournier
- Aix-Marseille Université, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - D Raoult
- Aix-Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
74
|
Mbogning Fonkou M, Mailhe M, Ndongo S, Ricaboni D, Morand A, Cornu F, Tidjani Alou M, Bilen M, Andrieu C, Levasseur A, Cadoret F, Raoult D. Noncontiguous finished genome sequences and descriptions of Actinomyces ihuae, Actinomyces bouchesdurhonensis, Actinomyces urinae, Actinomyces marseillensis, Actinomyces mediterranea and Actinomyces oralis sp. nov. identified by culturomics. New Microbes New Infect 2018; 25:30-44. [PMID: 29992027 PMCID: PMC6036942 DOI: 10.1016/j.nmni.2018.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 06/05/2018] [Accepted: 06/10/2018] [Indexed: 11/22/2022] Open
Abstract
The taxonogenomic approach, including the culturomics techniques, is now currently used to isolate and characterize new bacteria. These approaches notably allowed us to discover six new species of the Actinomyces genus: Actinomyces ihuae strain SD1, Actinomyces bouchesdurhonensis strain Marseille-P2825, Actinomyces urinae strain Marseille-P2225, Actinomyces marseillensis strain Marseille-P2818, Actinomyces mediterranea strain Marseille-P3257 and Actinomyces oralis strain Marseille-P3109. Each is the type strain of the corresponding bacterial species. 16S ribosomal RNA gene sequence comparison was used to classify these strains among the Actinomyces genus. These strains are all Gram positive, rod shaped and facultative aerobic. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - D. Raoult
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| |
Collapse
|
75
|
Dione N, Bellali S, Yasir M, Azhar EI, Bibi F, Beye M, Armstrong N, Cadoret F, Jiman-Fatani AA, Helmy N, Rathored J, Labas N, Fournier PE, Raoult D, Lagier JC. Anaerococcus jeddahensis sp. nov., a New Bacterial Species Isolated From Healthy Nomadic Bedouin Woman From Saudi Arabia. Curr Microbiol 2018; 75:1419-1428. [PMID: 29982935 DOI: 10.1007/s00284-018-1538-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 07/05/2018] [Indexed: 12/19/2022]
Abstract
An understanding of the microbial diversity of the human body has generated significant interest in recent years. With the advent of MALDI-TOF mass spectrometry, high-speed sequencing, and the rebirth of microbial culture, knowledge of human microbiota is growing. Using culturomics, a strategy to explore the microbial diversity of samples, coupled with a taxono-genomic strategy, we isolated a new bacterium named Anaerococcus jeddahensis sp. nov. strain SB3T. This strain was isolated from the stool sample of a healthy nomadic Bedouin woman from Saudi Arabia. Here, we describe the characteristics of this organism, and the complete genome sequence and annotation. Strain SB3T is a Gram-positive obligate anaerobic coccus which is non-motile and non-spore forming. Fatty acid analysis shows that the major fatty acid is by far hexadecanoic acid (C16:0; 52%). Its genome is 1,903,534 bp long and has 29.70 mol% of G+C content. It contains 1756 protein-coding genes and 53 RNA genes. These results show that strategy provides a better understanding of the microorganism and that is a good methodology for microbial identification and characterization.
Collapse
Affiliation(s)
- Niokhor Dione
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sara Bellali
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Muhammad Yasir
- 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.,Departments of Medical Laboratory Technology and Medical Microbiology and Parasitology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mamadou Beye
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Frédéric Cadoret
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Asif A Jiman-Fatani
- Departments of Medical Laboratory Technology and Medical Microbiology and Parasitology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Nayel Helmy
- Department of Obstetrics and Gynecology, Suliman Fageeh Hospital, Jeddah, Saudi Arabia
| | - Jaishriram Rathored
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Noémie Labas
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | | | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, IHU Méditerranée Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | | |
Collapse
|
76
|
Diop K, Diop A, Michelle C, Richez M, Rathored J, Bretelle F, Fournier PE, Fenollar F. Description of three new Peptoniphilus species cultured in the vaginal fluid of a woman diagnosed with bacterial vaginosis: Peptoniphilus pacaensis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilus vaginalis sp. nov. Microbiologyopen 2018; 8:e00661. [PMID: 29931836 PMCID: PMC6436483 DOI: 10.1002/mbo3.661] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/05/2018] [Accepted: 04/30/2018] [Indexed: 12/19/2022] Open
Abstract
Three previously unidentified Gram‐positive anaerobic coccoid bacteria, strains KhD‐2T, KHD4T, and Kh‐D5T, isolated from a vaginal swab, were characterized using the taxonogenomics concept. The phylogenic analysis, phenotypic characteristics, and genotypic data presented in this report attest that these three bacteria are distinct from previously known bacterial species with standing in nomenclature and represent three new Peptoniphilus species. Strain KhD‐2T is most closely related to Peptoniphilus sp. DNF00840 and Peptoniphilus harei (99.7% and 98.2% identity, respectively); strain KHD4T to Peptoniphilus lacrimalis (96%) and strain Kh‐D5T to Peptoniphilus coxii (97.2%). Strains KhD‐2T, KHD4T, and Kh‐D5TDNA G+C contents are, respectively, 34.23%, 31.87%, and 49.38%; their major fatty acid was C16:0 (41.6%, 32.0%, and 36.4%, respectively). We propose that strains KhD‐2T (=CSUR P0125 = DSM 101742), KHD4T (=CSUR P0110 = CECT 9308), and Kh‐D5T (=CSUR P2271 = DSM 101839) be the type strains of the new species for which the names Peptoniphilus vaginalis sp. nov., Peptoniphilus raoultii sp. nov., and Peptoniphilu pacaensis sp. nov., are proposed, respectively.
Collapse
Affiliation(s)
- Khoudia Diop
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Awa Diop
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Caroline Michelle
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Magali Richez
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Jaishriram Rathored
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Florence Bretelle
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Department of Gynecology and Obstetrics, Gynépole, Hôpital Nord, AP-HM, Marseille, France
| | | | - Florence Fenollar
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| |
Collapse
|
77
|
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.
Collapse
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
| |
Collapse
|
78
|
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.
Collapse
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
| |
Collapse
|
79
|
Togo AH, Diop A, Million M, Maraninchi M, Lagier JC, Robert C, Di Pinto F, Raoult D, Fournier PE, Bittar F. Draft Genome and Description of Eisenbergiella massiliensis Strain AT11 T: A New Species Isolated from Human Feces After Bariatric Surgery. Curr Microbiol 2018; 75:1274-1281. [PMID: 29858619 DOI: 10.1007/s00284-018-1520-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/29/2018] [Indexed: 12/19/2022]
Abstract
A novel strain of a Gram-stain negative, non-motile, non-spore forming rod-shaped, obligate anaerobic bacterium, designated AT11T, was isolated from a stool sample of a morbidly obese woman living in Marseille, France. This bacterium was characterized using biochemical, chemotaxonomic, and phylogenetic methods. The 16S rRNA gene sequence analysis showed that strain AT11T had a 97.8% nucleotide sequence similarity with Eisenbergiella tayi strain B086562T, the closest species with standing in nomenclature. The major cellular fatty acids of the novel isolate were C16:0 followed by saturated or unsaturated C18 fatty acids (C18:1n9, C18:1n5 and C18:0). The draft genome of strain AT11T is 7,114,554 bp long with 48% G+C content. 6176 genes were predicted, including 6114 protein-coding genes and 62 were RNAs (with 2 5S rRNA genes, two 16S rRNA genes, two 23S rRNA genes, and 56 tRNA genes). The digital DNA-DNA hybridization (dDDH) relatedness between the new isolate and E. tayi strain B086562T was 23.1% ± 2.2. Based on the phenotypic, chemotaxonomic, genomic, and phylogenetic characteristics, Eisenbergiella massiliensis sp. nov., is proposed. The type strain is AT11T (= DSM 100838T = CSUR P2478T).
Collapse
Affiliation(s)
- Amadou H Togo
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Awa Diop
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Matthieu Million
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Marie Maraninchi
- Aix Marseille Univ, NORT "Nutrition, Obesity and Risk of Thrombosis", INSERM1062, INRA1260, 13385, Marseille, France
| | | | - Catherine Robert
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France
| | - Fabrizio Di Pinto
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | | | - Fadi Bittar
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France.
- IHU-Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.
| |
Collapse
|
80
|
Description of Mediterraneibacter massiliensis, gen. nov., sp. nov., a new genus isolated from the gut microbiota of an obese patient and reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus and Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., Mediterraneibacter lactaris comb. nov., Mediterraneibacter torques comb. nov., Mediterraneibacter gnavus comb. nov. and Mediterraneibacter glycyrrhizinilyticus comb. nov. Antonie van Leeuwenhoek 2018; 111:2107-2128. [PMID: 29855844 DOI: 10.1007/s10482-018-1104-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/20/2018] [Indexed: 12/20/2022]
Abstract
An anaerobic isolate, strain AT7T, was cultivated from a stool sample of a morbidly obese French woman using a microbial culturomics approach. The 16S rRNA gene sequence analysis showed that strain AT7T exhibited 96% nucleotide sequence similarity with Ruminococcus torques strain JCM 6553T (= ATCC 27756T = VPI B2-51T), currently the closest related species with a validly published name. The strain was observed to be a Gram-stain positive, non-motile, asporogenous and coccobacillary-shaped bacterium. It was found to be catalase positive and oxidase negative. Its major fatty acids were identified as C16:0 (54%) and C18:1n9 (30%). The draft genome of strain AT7T is 3,069,882 bp long with 42.4% G+C content. 2925 genes were predicted, including 2867 protein-coding genes and 58 RNAs. Based on phenotypic, biochemical, phylogenetic and genomic evidence, we propose the creation of the new genus Mediterraneibacter and species, Mediterraneibacter massiliensis, that contains strain AT7T (= CSUR P2086T = DSM 100837T), and the reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus, Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., with type strain Eg2T (= KCTC 5757T = JCM15917T), Mediterraneibacter lactaris comb. nov., with type strain ATCC 29176T (= VPI X6-29T), Mediterraneibacter torques comb. nov., with type strain ATCC 27756T (= VPI B2-51T), Mediterraneibacter gnavus comb. nov., with type strain ATCC 29149T (= VPI C7-9T) and Mediterraneibacter glycyrrhizinilyticus comb. nov., with type strain ZM35T (= JCM 13368T = DSM 17593T), respectively.
Collapse
|
81
|
Zhang Q, Yu Z, Wang X, Tian J. Effects of inoculants and environmental temperature on fermentation quality and bacterial diversity of alfalfa silage. Anim Sci J 2018; 89:1085-1092. [DOI: 10.1111/asj.12961] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 10/11/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Qing Zhang
- College of Forestry and Landscape Architecture; South China Agricultural University; Guangzhou China
- College of Animal Science and Technology; China Agricultural University; Beijing China
| | - Zhu Yu
- College of Animal Science and Technology; China Agricultural University; Beijing China
| | - Xianguo Wang
- College of Animal Science and Technology; China Agricultural University; Beijing China
| | - Jipeng Tian
- College of Animal Science and Technology; China Agricultural University; Beijing China
| |
Collapse
|
82
|
Diop K, Diop A, Khelaifia S, Robert C, Pinto FD, Delerce J, Raoult D, Fournier PE, Bretelle F, Fenollar F. Characterization of a novel Gram-stain-positive anaerobic coccus isolated from the female genital tract: Genome sequence and description of Murdochiella vaginalis sp. nov. Microbiologyopen 2018; 7:e00570. [PMID: 29745065 PMCID: PMC6011929 DOI: 10.1002/mbo3.570] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022] Open
Abstract
Strain Marseille-P2341T , a nonmotile, nonspore-forming, Gram-stain-positive anaerobic coccus, was isolated in the vaginal specimen of a patient with bacterial vaginosis using culturomics. Its growth occurred at temperatures ranging from 25 to 42°C, with pH between 6.5 and 8.5, and at NaCl concentrations lower than 5%. The major fatty acids were C18:1n9 (27.7%) and C16:0 (24.4%). Its genome is 1,671,491 bp long with 49.48 mol% of G+C content. It is composed of 1,501 genes: 1,446 were protein-coding genes and 55 were RNAs. Strain Marseille-P2341T shared 97.3% of 16S rRNA gene sequence similarity with Murdochiella asaccharolytica, the phylogenetically closest species. These results enabled the classification of strain Marseille-P2341T as a new species of the genus Murdochiella for which we proposed the name Murdochiella vaginalis sp. nov. The type strain is strain Marseille-P2341T (=DSM 102237, =CSUR P2341).
Collapse
Affiliation(s)
- Khoudia Diop
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Marseille, France
| | - Awa Diop
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Marseille, France
| | - Saber Khelaifia
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Marseille, France
| | - Catherine Robert
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Marseille, France
| | - Fabrizio Di Pinto
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Marseille, France
| | - Jérémy Delerce
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Marseille, France
| | - Didier Raoult
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, 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 Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Marseille, France
| | - Florence Bretelle
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Marseille, France.,Department of Gynecology and Obstetrics, Gynépole, Marseille, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Florence Fenollar
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR 7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Marseille, France
| |
Collapse
|
83
|
Ndongo S, Bittar F, Beye M, Robert C, Di Pinto F, Fournier PE, Raoult D, Lagier JC. 'Cellulomonas timonensis' sp. nov., taxonogenomics description of a new bacterial species isolated from human gut. New Microbes New Infect 2018; 23:7-16. [PMID: 29692905 PMCID: PMC5913061 DOI: 10.1016/j.nmni.2018.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 01/26/2018] [Indexed: 12/22/2022] Open
Abstract
'Cellulomonas timonensis' sp. nov. strain sn7T is a new species within the Cellulomonas genus. We present the main phenotypic characteristics and provide a complete annotation of its genome sequence. This facultative anaerobic bacterium, isolated from the stool of 38-year-old obese Frenchman, is Gram-positive, has motile rods and is sporulating. The genome is 4 057 828 bp long with 72.42% G + C content. Of the 3732 predicted genes, 3667 were protein-coding genes and 65 were RNAs.
Collapse
Affiliation(s)
- S. Ndongo
- Aix-Marseille Université, IRD, AP-HM, IHU-Méditerranée Infection, UMR Microbes Evolution Phylogénie (MEPHI), Marseille, France
| | - F. Bittar
- Aix Marseille Univ, IRD (Dakar, Marseille, Papeete), AP-HM, IHU-Méditerranée Infection, UMR Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - M. Beye
- Aix Marseille Univ, IRD (Dakar, Marseille, Papeete), AP-HM, IHU-Méditerranée Infection, UMR Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - C. Robert
- Aix-Marseille Université, IRD, AP-HM, IHU-Méditerranée Infection, UMR Microbes Evolution Phylogénie (MEPHI), Marseille, France
| | - F. Di Pinto
- Aix-Marseille Université, IRD, AP-HM, IHU-Méditerranée Infection, UMR Microbes Evolution Phylogénie (MEPHI), Marseille, France
| | - P.-E. Fournier
- Aix Marseille Univ, IRD (Dakar, Marseille, Papeete), AP-HM, IHU-Méditerranée Infection, UMR Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - D. Raoult
- Aix-Marseille Université, IRD, AP-HM, IHU-Méditerranée Infection, UMR Microbes Evolution Phylogénie (MEPHI), Marseille, France
| | - J.-C. Lagier
- Aix-Marseille Université, IRD, AP-HM, IHU-Méditerranée Infection, UMR Microbes Evolution Phylogénie (MEPHI), Marseille, France
| |
Collapse
|
84
|
Seck EH, Diop A, Armstrong N, Delerce J, Fournier PE, Raoult D, Khelaifia S. Microbial culturomics to isolate halophilic bacteria from table salt: genome sequence and description of the moderately halophilic bacterium Bacillus salis sp. nov. New Microbes New Infect 2018; 23:28-38. [PMID: 29707210 PMCID: PMC5917939 DOI: 10.1016/j.nmni.2017.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/13/2017] [Accepted: 12/20/2017] [Indexed: 11/15/2022] Open
Abstract
Bacillus salis strain ES3T (= CSUR P1478 = DSM 100598) is the type strain of B. salis sp. nov. It is an aerobic, Gram-positive, moderately halophilic, motile and spore-forming bacterium. It was isolated from commercial table salt as part of a broad culturomics study aiming to maximize the culture conditions for the in-depth exploration of halophilic bacteria in salty food. Here we describe the phenotypic characteristics of this isolate, its complete genome sequence and annotation, together with a comparison with closely related bacteria. Phylogenetic analysis based on 16S rRNA gene sequences indicated 97.5% similarity with Bacillus aquimaris, the closest species. The 8 329 771 bp long genome (one chromosome, no plasmids) exhibits a G+C content of 39.19%. It is composed of 18 scaffolds with 29 contigs. Of the 8303 predicted genes, 8109 were protein-coding genes and 194 were RNAs. A total of 5778 genes (71.25%) were assigned a putative function.
Collapse
Affiliation(s)
- E H Seck
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - A Diop
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - N Armstrong
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - J Delerce
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - P-E Fournier
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| | - D Raoult
- URMITE, 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
| | - S Khelaifia
- URMITE, UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, Aix-Marseille Université, Marseille, France
| |
Collapse
|
85
|
Khelaifia S, Caputo A, Andrieu C, Cadoret F, Armstrong N, Michelle C, Lagier JC, Djossou F, Fournier PE, Raoult D. Genome sequence and description of Haloferax massiliense sp. nov., a new halophilic archaeon isolated from the human gut. Extremophiles 2018; 22:485-498. [PMID: 29435649 PMCID: PMC5862939 DOI: 10.1007/s00792-018-1011-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 02/05/2018] [Indexed: 12/22/2022]
Abstract
By applying the culturomics concept and using culture conditions containing a high salt concentration, we herein isolated the first known halophilic archaeon colonizing the human gut. Here we described its phenotypic and biochemical characterization as well as its genome annotation. Strain Arc-HrT (= CSUR P0974 = CECT 9307) was mesophile and grew optimally at 37 °C and pH 7. Strain Arc-HrT was also extremely halophilic with an optimal growth observed at 15% NaCl. It showed gram-negative cocci, was strictly aerobic, non-motile and non-spore-forming, and exhibited catalase and oxidase activities. The 4,015,175 bp long genome exhibits a G + C% content of 65.36% and contains 3911 protein-coding and 64 predicted RNA genes. PCR-amplified 16S rRNA gene of strain Arc-HrT yielded a 99.2% sequence similarity with Haloferax prahovense, the phylogenetically closest validly published species in the Haloferax genus. The DDH was of 50.70 ± 5.2% with H. prahovense, 53.70 ± 2.69% with H. volcanii, 50.90 ± 2.64% with H. alexandrinus, 52.90 ± 2.67% with H. gibbonsii and 54.30 ± 2.70% with H. lucentense. The data herein represented confirm strain Arc-HrT as a unique species and consequently we propose its classification as representative of a novel species belonging to the genus Haloferax, as Haloferax massiliense sp. nov.
Collapse
Affiliation(s)
- Saber Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France.
| | - Aurelia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Claudia Andrieu
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Frederique Cadoret
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Nicholas Armstrong
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Caroline Michelle
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Felix Djossou
- Infectious and Tropical Diseases Department, Centre Hospitalier Andrée-Rosemon, Cayenne, French Guiana
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, CNRS, (UMR 7278) IRD (198), INSERM (U1095), AMU (UM63), Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 5, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
86
|
Diop A, Seck EH, Dubourg G, Armstrong N, Blanc-Tailleur C, Raoult D, Fournier PE. Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481 T , a moderate halophilic bacterium isolated from the human gut microflora. Microbiologyopen 2018; 8:e00638. [PMID: 29675845 PMCID: PMC6485780 DOI: 10.1002/mbo3.638] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/31/2018] [Accepted: 03/09/2018] [Indexed: 12/19/2022] Open
Abstract
Microbial culturomics represents an ongoing revolution in the characterization of the human gut microbiota. By using three culture media containing high salt concentrations (10, 15, and 20% [w/v] NaCl), we attempted an exhaustive exploration of the halophilic microbial diversity of the human gut and isolated strain Marseille‐P2481 (= CSUR P2481 = DSM 103076), a new moderately halophilic bacterium. This bacterium is a Gram‐positive, strictly aerobic, spore‐forming rod that is motile by use of a flagellum and exhibits catalase, but not oxidase activity. Strain Marseille‐P2481 was cultivated in media containing up to 20% (w/v) NaCl, with optimal growth being obtained at 37°C, pH 7.0–8.0, and 7.5% [w/v] NaCl). The major fatty acids were 12‐methyl‐tetradecanoic acid and hexadecanoic acid. Its draft genome is 4,548,390 bp long, composed of 11 scaffolds, with a G+C content of 39.8%. It contains 4,335 predicted genes (4,266 protein coding including 89 pseudogenes and 69 RNA genes). Strain Marseille‐P2481 showed 96.57% 16S rRNA sequence similarity with Gracilibacillus alcaliphilus strain SG103T, the phylogenetically closest species with standing in nomenclature. On the basis of its specific features, strain Marseille‐P2481T was classified as type strain of a new species within the genus Gracilibacillus for which the name Gracilibacillus timonensis sp. nov. is formally proposed.
Collapse
Affiliation(s)
- Awa Diop
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - El Hadji Seck
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - Gregory Dubourg
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - Nicholas Armstrong
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - Caroline Blanc-Tailleur
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| | - Didier Raoult
- URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, 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 U1095, Aix-Marseille Université, Institut hospitalo-universitaire Mediterranee-infection, Marseille, France
| |
Collapse
|
87
|
Afouda P, Durand GA, Lagier JC, Labas N, Cadoret F, Armstrong N, Raoult D, Dubourg G. Noncontiguous finished genome sequence and description of Intestinimonas massiliensis sp. nov strain GD2 T , the second Intestinimonas species cultured from the human gut. Microbiologyopen 2018; 8:e00621. [PMID: 29654664 PMCID: PMC6341035 DOI: 10.1002/mbo3.621] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 01/08/2023] Open
Abstract
Intestinimonas massiliensis sp. nov strain GD2T is a new species of the genus Intestinimonas (the second, following Intestinimonas butyriciproducens gen. nov., sp. nov). First isolated from the gut microbiota of a healthy subject of French origin using a culturomics approach combined with taxono-genomics, it is strictly anaerobic, nonspore-forming, rod-shaped, with catalase- and oxidase-negative reactions. Its growth was observed after preincubation in an anaerobic blood culture enriched with sheep blood (5%) and rumen fluid (5%), incubated at 37°C. Its phenotypic and genotypic descriptions are presented in this paper with a full annotation of its genome sequence. This genome consists of 3,104,261 bp in length and contains 3,074 predicted genes, including 3,012 protein-coding genes and 62 RNA-coding genes. Strain GD2T significantly produces butyrate and is frequently found among available 16S rRNA gene amplicon datasets, which leads consideration of Intestinimonas massiliensis as an important human gut commensal.
Collapse
Affiliation(s)
- Pamela Afouda
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Guillaume A Durand
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jean-Christophe Lagier
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Noémie Labas
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Fréderic Cadoret
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Nicholas Armstrong
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Grégory Dubourg
- Microbes, Evolution, Phylogeny and Infection, Aix-Marseille Université, UM 63, CNRS 7278, IRD 198, Inserm 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France
| |
Collapse
|
88
|
Beye M, Bakour S, Traore SI, Rathored J, Labas N, Raoult D, Fournier PE. Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut. Stand Genomic Sci 2018; 13:8. [PMID: 29682169 PMCID: PMC5896035 DOI: 10.1186/s40793-018-0310-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 03/21/2018] [Indexed: 11/10/2022] Open
Abstract
We report the properties of a draft genome sequence of the bacterium Fermentimonas caenicola strain SIT8 (= CSUR P1560). This strain, whose genome is described here, was isolated from the fecal flora of a healthy 28-month-old Senegalese boy. Strain SIT8 is a facultatively anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,824,451-bp long (1 chromosome but no plasmid) contains 2354 protein-coding and 46 RNA genes, including four rRNA genes.
Collapse
Affiliation(s)
- Mamadou Beye
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
| | - Sofiane Bakour
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
| | - Sory Ibrahima Traore
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
| | - Jaishriram Rathored
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
| | - Noémie Labas
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
| | - Didier Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 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, Inserm1095, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-infection, 19-21 Bd Jean Moulin, 13385 Marseille, cedex 5 France
| |
Collapse
|
89
|
Senghor B, Bassène H, Khelaifia S, Robert C, Fournier PE, Ruimy R, Sokhna C, Raoult D, Lagier JC. Sediminibacillus massiliensis sp. nov., a moderately halophilic, Gram-positive bacterium isolated from a stool sample of a young Senegalese man. Antonie van Leeuwenhoek 2018; 111:1225-1236. [PMID: 29417358 DOI: 10.1007/s10482-018-1032-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 01/27/2018] [Indexed: 01/26/2023]
Abstract
A Gram-positive, moderately halophilic bacterium, referred to as strain Marseille-P3518T, was isolated from a stool sample with 2% NaCl concentration from a healthy 15-year-old male living in Dielmo, a village in Senegal. Cells are aerobic, rod-shaped and motile and display endospore formation. Strain Marseille-P3518T can grow in a medium with 0-20% (w/v) sodium chloride (optimally at 5-7.5% w/v). The major fatty acids were 12-methyl-tetradecanoic acid (45.8%), 13-methyl-tetradecanoic acid (26.9%) and 12-methyl-tridecanoic acid (12.8%). The genome is 4,347,479 bp long with 42.1% G+C content. It contains 4282 protein-coding and 107 RNA genes. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that strain Marseille-P3518T is a member of the Bacillaceae family and is closely related to Sediminibacillus albus (97.4% gene sequence similarity). Strain Marseille-P3518T was clearly differentiated from its phylogenetic neighbors on the basis of phenotypic and genotypic features. Strain Marseille-P3518T is, therefore, considered to be a novel representative of the genus Sediminibacillus, for which the name Sediminibacillus massiliensis sp. nov. is proposed, and the type strain is Marseille-P3518T (CSUR P3518T, DSM69894).
Collapse
Affiliation(s)
- Bruno Senghor
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Hubert Bassène
- 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
| | - Saber Khelaifia
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Catherine Robert
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre-Edouard Fournier
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Raymond Ruimy
- Department of Bacteriology at Nice, Academic Hospital, Nice, France.,Nice Medical University, Nice-Sophia Antipolis University, Nice, France.,INSERM U1065 (C3M), Bacterial Toxins in Host Pathogen Interactions, C3M, Bâtiment Universitaire Archimed, Nice, France
| | - Cheikh 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
| | - Didier Raoult
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jedda, Saudi Arabia
| | - Jean-Christophe Lagier
- URMITE, Aix Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU - Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
| |
Collapse
|
90
|
Corynebacterium fournierii sp. nov., isolated from the female genital tract of a patient with bacterial vaginosis. Antonie van Leeuwenhoek 2018; 111:1165-1174. [PMID: 29383461 DOI: 10.1007/s10482-018-1022-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/23/2018] [Indexed: 12/22/2022]
Abstract
Strain Marseille-P2948T, a novel Gram-positive, catalase-positive bacterium was isolated from a vaginal sample of a patient with bacterial vaginosis. It was characterised using the taxonogenomic approach. Phylogenetic analysis revealed that the 16S rRNA and the rpoB genes exhibit 98.7 and 93.4% similarity, respectively, with those of Corynebacterium ureicelerivorans strain IMMIB RIV-301T. Biochemical tests of strain Marseille-P2948T gave results that were similar to those of other validly named Corynebacterium species, whereas chemotaxonomic tests showed the presence of C16:0, C18:1n9, C18:0, and C18:2n6 in the fatty acid profile. The draft genome of strain Marseille-P2948T is 2,383,644 bp long in size with a G+C content of 65.03%. Of the 2210 predicted genes, 2147 are protein-coding genes and 63 are RNAs. Based on phenotypic, phylogenic and genomic results, it was concluded that the isolate represents a new species within the genus Corynebacterium. The name Corynebacterium fournierii sp. nov. is proposed and the type strain is Marseille-P2948T (= CSUR P2948 = DSM 103271).
Collapse
|
91
|
Leangapichart T, Gautret P, Nguyen T, Armstrong N, Rolain JM. Genome sequence of " Leucobacter massiliensis" sp. nov. isolated from human pharynx after travel to the 2014 Hajj. New Microbes New Infect 2018; 21:42-48. [PMID: 29204283 PMCID: PMC5709290 DOI: 10.1016/j.nmni.2017.10.007] [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: 06/26/2017] [Revised: 10/09/2017] [Accepted: 10/17/2017] [Indexed: 01/12/2023] Open
Abstract
"Leucobacter massiliensis" strain 122RC15T sp. nov. is a new species within the genus Leucobacter. The genome of this strain is described here. It was isolated from the pharynx of a 76-year-old Algerian female after travelling from the 2014 Hajj. "Leucobacter massiliensis" is a Gram-positive, aerobic bacillus. Here we describe the features including complete genome and annotation of this strain. The 3 136 406-bp long genome contains 2797 protein-coding genes and 49 RNA genes.
Collapse
Affiliation(s)
| | | | | | | | - J.-M. Rolain
- Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE) CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France
| |
Collapse
|
92
|
Ngom I, Mailhe M, Ricaboni D, Vitton V, Benezech A, Khelaifia S, Michelle C, Cadoret F, Armstrong N, Levasseur A, Raoult D, Million M. Noncontiguous finished genome sequence and description of Mediterranea massiliensis gen. nov., sp. nov., a new member of the Bacteroidaceae family isolated from human colon. New Microbes New Infect 2018; 21:105-116. [PMID: 29321938 PMCID: PMC5751998 DOI: 10.1016/j.nmni.2017.11.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/17/2017] [Accepted: 11/27/2017] [Indexed: 12/22/2022] Open
Abstract
Strain Marseille-P2645T was isolated in a colon sample from a Frenchwoman who underwent a colonoscopy. Bacterial cells were Gram negative, non-spore forming, mobile and strictly anaerobic. The genome of strain Marseille-P2645T is 3 950 441 bp long and contains 3374 protein-coding genes. The DNA G+C content is of 51.66 mol%. Strain Marseille-P2645T exhibited a 92.9% sequence similarity with Bacteroides helcogenes strain P36-108T (GenBank accession no. CP002352), the phylogenetically closest species with standing in nomenclature. Strain Marseille-P2645T (= CSUR P2645 = DSM 103034) is therefore a candidate as a type species of a new genus belonging to the Bacteroidaceae family, for which the name of Mediterranea massiliensis gen. nov., sp. nov., is proposed.
Collapse
Affiliation(s)
- I.I. Ngom
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - M. Mailhe
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - D. Ricaboni
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - V. Vitton
- Service de Gastroentérologie, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - A. Benezech
- Service de Gastroentérologie, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - S. Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - C. Michelle
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - F. Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - N. Armstrong
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - A. Levasseur
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| | - M. Million
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, France
| |
Collapse
|
93
|
Alou M, Ndongo S, Frégère L, Labas N, Andrieu C, Richez M, Couderc C, Baudoin JP, Abrahão J, Brah S, Diallo A, Sokhna C, Cassir N, La Scola B, Cadoret F, Raoult D. Taxonogenomic description of four new Clostridium species isolated from human gut: 'Clostridium amazonitimonense', 'Clostridium merdae', 'Clostridium massilidielmoense' and 'Clostridium nigeriense'. New Microbes New Infect 2018; 21:128-139. [PMID: 29348922 PMCID: PMC5767839 DOI: 10.1016/j.nmni.2017.11.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/09/2017] [Accepted: 11/16/2017] [Indexed: 12/29/2022] Open
Abstract
Culturomics investigates microbial diversity of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. The present study allowed identification of four putative new Clostridium sensu stricto species: 'Clostridium amazonitimonense' strain LF2T, 'Clostridium massilidielmoense' strain MT26T, 'Clostridium nigeriense' strain Marseille-P2414T and 'Clostridium merdae' strain Marseille-P2953T, which we describe using the concept of taxonogenomics. We describe the main characteristics of each bacterium and present their complete genome sequence and annotation.
Collapse
Affiliation(s)
- M.T. Alou
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - S. Ndongo
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - L. Frégère
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - N. Labas
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - C. Andrieu
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - M. Richez
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - C. Couderc
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - J.-P. Baudoin
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - J. Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - S. Brah
- Hopital National de Niamey, BP 247, Niamey, Niger
| | - A. Diallo
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Campus Commun UCAD-IRD of Hann, Route des pères Maristes, Hann Maristes, BP 1386, CP 18524, Dakar, Senegal
| | - C. Sokhna
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Campus Commun UCAD-IRD of Hann, Route des pères Maristes, Hann Maristes, BP 1386, CP 18524, Dakar, Senegal
| | - N. Cassir
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - B. La Scola
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - F. Cadoret
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
94
|
Diop K, Andrieu C, Michelle C, Armstrong N, Bittar F, Bretelle F, Fournier PE, Raoult D, Fenollar F. Characterization of a New Ezakiella Isolated from the Human Vagina: Genome Sequence and Description of Ezakiella massiliensis sp. nov. Curr Microbiol 2017; 75:456-463. [PMID: 29188320 DOI: 10.1007/s00284-017-1402-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 11/16/2017] [Indexed: 12/12/2022]
Abstract
The study of the vaginal microbiota using the "culturomics concept" allowed us to isolate, from the vaginal swab of an asymptomatic 20-year-old woman who had sexual relations with another woman with bacterial vaginosis, an unknown Gram-positive anaerobic coccus-shaped bacterium that was designated strain Marseille-P2951T and characterized using taxono-genomics. Strain Marseille-P2951T is non-motile and non-spore forming and exhibits catalase and oxidase activities. Its 16S rRNA gene-based identification showed 98.5% identity with Ezakiella peruensis, the phylogenetically closest species. The major fatty acids are C18:1n9 (58%) and C16:0 (22%). With a 1,741,785 bp length, the G+C content of the genome is 36.69%. Of a total of 1657 genes, 1606 are protein-coding genes and 51 RNAs. Also, 1123 genes are assigned a putative function and 127 are ORFans. Phenotypic, phylogenetic, and genomics analyses revealed that strain Marseille-P2951T (=CSUR P2951 =DSM 103122) is distinct and represents a new species of the genus Ezakiella, for which the name Ezakiella massiliensis sp. nov. is proposed.
Collapse
Affiliation(s)
- Khoudia Diop
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France
| | - Claudia Andrieu
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France
| | - Caroline Michelle
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France
| | - Nicholas Armstrong
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France
| | - Fadi Bittar
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France
| | - Florence Bretelle
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France.,Department of Gynecology and Obstetrics, Gynépole, Marseille, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, AMU, Aix-Marseille Université, Marseille Cedex 05, France
| | - Pierre-Edouard Fournier
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France
| | - Didier Raoult
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Florence Fenollar
- Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, AMU UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de Médecine, 19-21 Boulevard Jean Moulin, 13005, Marseille Cedex 05, France.
| |
Collapse
|
95
|
Pham TPT, Tidjani Alou M, Traore S, Brah S, Ali Diallo B, Diallo A, Sokhna C, Baptiste E, Levasseur A, Fournier PE, Cadoret F, Raoult D. Noncontiguous finished genome sequences and descriptions of 'Paenibacillus bouchesdurhonensis,' 'Paenibacillus rubinfantis,' 'Paenibacillus senegalimassiliensis' and 'Paenibacillus tuaregi' identified by culturomics. New Microbes New Infect 2017; 20:1-13. [PMID: 28912952 PMCID: PMC5583396 DOI: 10.1016/j.nmni.2017.07.004] [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: 04/26/2017] [Revised: 06/14/2017] [Accepted: 07/05/2017] [Indexed: 12/22/2022] Open
Abstract
Microbial culturomics represents a completely new approach to investigate microbial diversity by using different optimized culture conditions, mass spectrometry, genome sequencing and annotation and phenotypic description that allow for an extensive characterization of new species and the study of the human microbiome. Here we present four new species within the genus Paenibacillus: 'Paenibacillus bouchesdurhonensis' strain Marseille-P3071T, 'Paenibacillus rubinfantis' strain MT18T, 'Paenibacillus senegalimassiliensis' strain SIT18T and 'Paenibacillus tuaregi' strain Marseille-P2472T, which are all facultatively aerobic and Gram-positive bacilli.
Collapse
Affiliation(s)
- T.-P.-T. Pham
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille, France
| | - M. Tidjani Alou
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille, France
| | - S.I. Traore
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille, France
| | - S. Brah
- Service de médecine interne, Hôpital National de Niamey, Niger
| | - B. Ali Diallo
- Laboratoire de Microbiologie, Département de Biologie, Université Abdou Moumouni de Niamey, Niamey, Niger
| | - A. Diallo
- Institut de Recherche pour le Développement, UMR 198 (URMITE), Campus International de Hann, Dakar, Sénégal
| | - C. Sokhna
- Institut de Recherche pour le Développement, UMR 198 (URMITE), Campus International de Hann, Dakar, Sénégal
| | - E. Baptiste
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille, France
| | - A. Levasseur
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille, France
| | - P.-E. Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille, France
| | - F. Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille, France
| | - D. Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
96
|
Seck EH, Beye M, Traore SI, Khelaifia S, Michelle C, Couderc C, Brah S, Fournier PE, Raoult D, Bittar F. Bacillus kwashiorkori sp. nov., a new bacterial species isolated from a malnourished child using culturomics. Microbiologyopen 2017; 7. [PMID: 29076642 PMCID: PMC5822343 DOI: 10.1002/mbo3.535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/15/2017] [Indexed: 12/16/2022] Open
Abstract
Strain SIT6T was isolated from the fecal flora of a severely malnourished child as part of a broad “culturomics” study aiming to maximize the culture conditions for the in‐depth exploration of the human microbiota. An analysis of the 16S rRNA gene sequence showed that strain SIT6T shared 94.1% 16S rRNA gene sequence similarity with Bacillus thermoamylovorans DKPT (NR_029151), the phylogenetically closest type species. Colonies are creamy white, circular, 4–5 mm in diameter after cultivation at 37°C for 24 hr on 5% sheep blood‐enriched Colombia agar. Growth occurs at temperatures in the range of 25–56°C (optimally at 37°C). Strain SIT6T is a gram‐positive, facultative anaerobic rod and motile by means of peritrichous flagella and sporulating; it is catalase and oxidase positive. The 2,784,637‐bp‐long genome, composed of 16 contigs, has a G+C content of 35.19%. Of the 2,646 predicted genes, 2,572 were protein‐coding genes and 74 were RNAs. The major fatty acids are saturated species (15:0 iso, 16:0 and 17:0 anteiso). Of the 14 detected fatty acids, 11 are saturated, either linear or branched (iso and anteiso). Digital DNA–DNA hybridization (dDDH) estimation and average genomic identity of orthologous gene sequences (AGIOS) of the strain SIT6T against genomes of the type strains of related species ranged between 18.6% and 38.3% and between 54.77% and 65.50%, respectively. According to our taxonogenomics results, we propose the creation of Bacillus kwashiorkori sp. nov. that contains the type strain SIT6T (=CSUR P2452T, =DSM 29059T).
Collapse
Affiliation(s)
- El Hadji Seck
- Aix-Marseille Univ, CNRS 7278, AP-HM, IRD 198, INSERM 1095, URMITE, IHU Méditerranée Infection, Marseille, France
| | - Mamadou Beye
- Aix-Marseille Univ, CNRS 7278, AP-HM, IRD 198, INSERM 1095, URMITE, IHU Méditerranée Infection, Marseille, France
| | - Sory Ibrahima Traore
- Aix-Marseille Univ, CNRS 7278, AP-HM, IRD 198, INSERM 1095, URMITE, IHU Méditerranée Infection, Marseille, France
| | - Saber Khelaifia
- Aix-Marseille Univ, CNRS 7278, AP-HM, IRD 198, INSERM 1095, URMITE, IHU Méditerranée Infection, Marseille, France
| | - Caroline Michelle
- Aix-Marseille Univ, CNRS 7278, AP-HM, IRD 198, INSERM 1095, URMITE, IHU Méditerranée Infection, Marseille, France
| | - Carine Couderc
- Aix-Marseille Univ, CNRS 7278, AP-HM, IRD 198, INSERM 1095, URMITE, IHU Méditerranée Infection, Marseille, France
| | | | - Pierre-Edouard Fournier
- Aix-Marseille Univ, CNRS 7278, AP-HM, IRD 198, INSERM 1095, URMITE, IHU Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille Univ, CNRS 7278, AP-HM, IRD 198, INSERM 1095, URMITE, IHU Méditerranée Infection, Marseille, France.,King Fahd Medical Research Center, Special Infectious Agents Unit, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fadi Bittar
- Aix-Marseille Univ, CNRS 7278, AP-HM, IRD 198, INSERM 1095, URMITE, IHU Méditerranée Infection, Marseille, France
| |
Collapse
|
97
|
Poehlein A, Yutin N, Daniel R, Galperin MY. Proposal for the reclassification of obligately purine-fermenting bacteria Clostridium acidurici (Barker 1938) and Clostridium purinilyticum (Dürre et al. 1981) as Gottschalkia acidurici gen. nov. comb. nov. and Gottschalkiapurinilytica comb. nov. and of Eubacterium angustum (Beuscher and Andreesen 1985) as Andreesenia angusta gen. nov. comb. nov. in the family Gottschalkiaceae fam. nov. Int J Syst Evol Microbiol 2017; 67:2711-2719. [PMID: 28853681 PMCID: PMC5737214 DOI: 10.1099/ijsem.0.002008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several strictly anaerobic bacteria that are Gram-stain-positive have the ability to use uric acid as the sole source of carbon and energy. The phylogeny of three such species, Clostridium acidurici, Clostridium purinilyticum, and Eubacterium angustum, members of the Clostridium cluster XII that ferment purines, but not most amino acids or carbohydrates, has been re-examined, taking advantage of their recently sequenced genomes. Phylogenetic analyses, based on 16S rRNA gene sequences, protein sequences of RpoB and GyrB, and on a concatenated alignment of 50 ribosomal proteins, revealed tight clustering of C. acidurici and C. purinilyticum. Eubacterium angustum showed consistent association with C. acidurici and C. purinilyticum
, but differed from these two in terms of the genome size, G+C content of its chromosomal DNA and its inability to form spores. We propose reassigning C. acidurici and C. purinilyticum to the novel genus Gottschalkia as Gottschalkia acidurici gen. nov. comb. nov. (the type species of the genus) and Gottschalkia purinilytica comb. nov., respectively. Eubacterium angustum is proposed to be reclassified as Andreesenia angusta gen. nov. comb. nov. Furthermore, based on the phylogenetic data and similar metabolic properties, we propose assigning genera Gottschalkia and Andreesenia to the novel family Gottschalkiaceae. Metagenomic sequencing data indicate the widespread distibution of organisms falling within the radiation of the proposed family Gottschalkiaceae in terrestrial and aquatic habitats from upstate New York to Antarctica, most likely due to their ability to metabolize avian-produced uric acid.
Collapse
Affiliation(s)
- Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Natalya Yutin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| |
Collapse
|
98
|
Cadoret F, Alou M, Afouda P, Traore I, Bréchard L, Michelle C, Di Pinto F, Andrieu C, Delerce J, Levasseur A, Fournier PE, Raoult D. Noncontiguous finished genome sequences and description of Bacillus massiliglaciei, Bacillus mediterraneensis, Bacillus massilinigeriensis, Bacillus phocaeensis and Bacillus tuaregi, five new species identified by culturomics. New Microbes New Infect 2017; 19:45-59. [PMID: 28706723 PMCID: PMC5496451 DOI: 10.1016/j.nmni.2017.04.005] [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: 12/01/2016] [Revised: 04/06/2017] [Accepted: 04/13/2017] [Indexed: 11/02/2022] Open
Abstract
Microbial culturomics, which investigates microbial diversity by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rDNA identification, allowed to identify five new species within the Bacillus genus. Bacillus massiliglaciei strain Marseille-P2600T, Bacillus mediterraneensis strain Marseille-P2384T, Bacillus massilinigeriensis strain Marseille-P2366T, Bacillus tuaregi strain Marseille-P2489T and Bacillus phocaeensis strain SIT16T are each the type strain of the corresponding bacterial species. These strains, the genomes of which are described here, are facultative anaerobic Gram-positive bacilli. Here, we describe the main characteristics of each bacterium and present their complete genome sequence and annotation.
Collapse
Affiliation(s)
- F. Cadoret
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - M.T. Alou
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - P. Afouda
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - I.S. Traore
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - L. Bréchard
- 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
| | - F. Di Pinto
- 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
| | - J. Delerce
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, INSERM 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Marseille, France
| | - A. Levasseur
- 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
| |
Collapse
|
99
|
Oren A, Garrity GM. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2017; 66:4299-4305. [PMID: 27928990 DOI: 10.1099/ijsem.0.001585] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
Collapse
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 91904 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| |
Collapse
|
100
|
El Houmami N, Bakour S, Bzdrenga J, Rathored J, Seligmann H, Robert C, Armstrong N, Schrenzel J, Raoult D, Yagupsky P, Fournier PE. Isolation and characterization of Kingella negevensis sp. nov., a novel Kingella species detected in a healthy paediatric population. Int J Syst Evol Microbiol 2017; 67:2370-2376. [PMID: 28699877 DOI: 10.1099/ijsem.0.001957] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We herein report the isolation and characterization of 21 Gram-stain-negative strains cultivated from the oropharynx of healthy children in Israel and Switzerland. Initially described as small colony variants of Kingella kingae, phenotypic analysis, biochemical analysis, phylogenetic analysis based on sequencing of the partial 16S rRNA gene and five housekeeping genes (abcZ, adk, G6PD, groEL and recA), and whole genome sequencing and comparison between members of the genera Kingella and Neisseria provided evidence for assigning them to the genus Kingella. Cellular fatty acids included important amounts of C12 : 0, C14 : 0, C16 : 0 and C16 : 1n7. Digital DNA-DNA hybridization between the isolates Sch538T and K. kingae ATCC 23330T revealed relatedness of 19.9 %. Comparative analysis of 16S rRNA gene sequences available in GenBank allowed matches to strains isolated in the USA, suggesting a wider geographical distribution. A novel species named Kingella negevensis sp. nov. is proposed, as most strains have been isolated in the Negev, a desert region of southern Israel. The type strain is Sch538T (=CCUG 69806T=CSUR P957).
Collapse
Affiliation(s)
- Nawal El Houmami
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Sofiane Bakour
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Janek Bzdrenga
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Jaishiram Rathored
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Hervé Seligmann
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Catherine Robert
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Jacques Schrenzel
- Hôpitaux Universitaires de Genève, Service of Infectious Diseases and Service of Laboratory Medicine, Geneva, Switzerland
| | - Didier Raoult
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Pablo Yagupsky
- Clinical Microbiology Laboratory, Soroka University Medical Center, Beer-Sheva, Israel
| | - Pierre-Edouard Fournier
- Aix-Marseille University, UM63, CNRS 7278, IRD 198, Inserm 1095, URMITE, Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| |
Collapse
|