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Magdy Wasfy R, Zoaiter M, Bilen M, Tidjani Alou M, Lo CI, Bellali S, Caputo A, Alibar S, Andrieu C, Raoult D, Fournier PE, Million M. Description of Agathobaculum massiliense sp. nov., a new bacterial species prevalent in the human gut and predicted to produce indole and tryptophan based on genomic analysis. Antonie Van Leeuwenhoek 2023; 116:541-555. [PMID: 37029880 DOI: 10.1007/s10482-023-01824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/16/2023] [Indexed: 04/09/2023]
Abstract
The novel bacterial strain Marseille-P4005T was isolated from the stool sample of a healthy donor. It is a Gram-stain negative, non-motile, non-spore-forming rod. It grew optimally at 37 °C and at pH 7.0 on 5% sheep blood-enriched Columbia agar after preincubation in a blood-culture bottle supplemented with rumen and blood. This strain does not ferment monosaccharides (except D-tagatose), disaccharides, or polymeric carbohydrates. The major cellular fatty acids were hexadecenoic (24.6%), octadecanoic (22.8%), and tetradecanoic (20.1%) acids. Next-generation sequencing revealed a genome size of 3.2 Mbp with a 56.4 mol% G + C. Phylogenetic analysis based on the 16S rRNA gene highlighted Agathobaculum desmolans strain ATCC 43058T as the closest related strain. The OrthoANI, AAI, and digital DNA-DNA hybridization values were below the critical thresholds of 95%, 95-96%, and 70%, respectively, to define a novel bacterial species. Antibiotic resistance genes APH(3')-IIIa, erm(B), and tet(W) were detected with high identity percentages of 100%, 98.78%, and 97.18% for each gene, respectively. The APH(3')-IIIa gene confers resistance to amikacin, erm(B) gene confers resistance to erythromycin, lincomycin, and clindamycin, while tet(W) gene confers resistance to doxycycline and tetracycline. Based on KEGG BlastKOALA analyses, the annotation results showed that our strain could use glucose to produce L-lactate and pyruvate but not acetate or ethanol. Also, strain Marseille-P4005T was predicted to use phenylalanine to produce indole, a major intercellular signal molecule within the gut microbial ecosystem. Through having a gene coding for tryptophan synthase beta chain (trpB), strain Marseille-P4005T could produce L-tryptophan (an essential amino acid) from indole. Strain Marseille-P4005T showed its highest prevalence in the human gut (34.19%), followed by the reproductive system (17.98%), according to a query carried out on the Integrated Microbial NGS (IMNGS) platform. Based on phylogenetic, phenotypic, and genomic analyses, we classify strain Marseille-P4005T (= CSUR P4005 = CECT 9669), a novel species within the genus Agathobaculum, for which the name of Agathobaculum massiliense sp. nov. is proposed.
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Affiliation(s)
- Reham Magdy Wasfy
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
| | - Malak Zoaiter
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France
| | - Melhem Bilen
- Department of Bioengineering and ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Maryam Tidjani Alou
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
| | - Cheikh Ibrahima Lo
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France
| | - Sara Bellali
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
| | - Aurelia Caputo
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France
| | - Stéphane Alibar
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, 13005, Marseille, France
| | - Claudia Andrieu
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, 13005, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France
| | - Pierre Edouard Fournier
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France
- IRD, AP-HM, SSA, VITROME, Aix Marseille Univ, Marseille, France
- Assistance Publique-Hôpitaux de Marseille, 13005, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 19-12 Bd Jean Moulin, 13005, Marseille, France.
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ, 13005, Marseille, France.
- Assistance Publique-Hôpitaux de Marseille, 13005, Marseille, France.
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Bellali S, Haddad G, Pham TPT, Iwaza R, Ibrahim A, Armstrong N, Fadlane A, Couderc C, Diallo A, Sokhna C, Million M, Raoult D, Tidjani Alou M. Draft genomes and descriptions of Urmitella timonensis gen. nov., sp. nov. and Marasmitruncus massiliensis gen. nov., sp. nov., isolated from severely malnourished African children using culturomics. Antonie Van Leeuwenhoek 2022; 115:1349-1361. [PMID: 36149539 PMCID: PMC9584879 DOI: 10.1007/s10482-022-01777-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 08/27/2022] [Indexed: 11/25/2022]
Abstract
Two strains, designated as Marseille-P2918T and Marseille-P3646T, were isolated from a 14-week-old Senegalese girl using culturomics: Urmitella timonensis strain Marseille-P2918T (= CSUR P2918, = DSM 103634) and Marasmitruncus massiliensis strain Marseille-P3646T (= CSUR P3646, = CCUG72353). Both strains were rod-shaped, anaerobic, spore forming motile bacteria. The 16S rRNA gene sequences of strains Marseille-P2918T (LT598554) and Marseille-P3646T (LT725660) shared 93.25% and 94.34% identity with Tissierella praeacuta ATCC 25539T and Anaerotruncus colihominis CIP 107754T, their respective phylogenetically closest species with standing in nomenclature. Therefore, strain Marseille-P2918T is classified within the family Tissierellaceae and order Tissierellales whereas strain Marseille-P3646T is classified within the family Oscillospiraceae and order Eubacteriales. The genome of strain Marseille-P2918T had a size of 2.13 Mb with a GC content of 50.52% and includes six scaffolds and six contigs, and that of strain Marseille-P3646T was 3.76 Mbp long consisting of five contigs with a 50.04% GC content. The genomes of both strains presented a high percentage of genes encoding enzymes involved in genetic information and processing, suggesting a high growth rate and adaptability. These new taxa are extensively described and characterised in this paper, using the concept of taxono-genomic description.
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Affiliation(s)
- Sara Bellali
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Gabriel Haddad
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.,IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
| | - Thi-Phuong-Thao Pham
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Rim Iwaza
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.,IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
| | - Ahmad Ibrahim
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.,IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
| | - Nicholas Armstrong
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Amael Fadlane
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Carine Couderc
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | | | - Cheikh Sokhna
- Campus Commun UCAD-IRD of Hann, Dakar, Senegal.,Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Matthieu Million
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Didier Raoult
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.,IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille, France
| | - Maryam Tidjani Alou
- Aix Marseille Université, MEPHI, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France.
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Maaloum M, Lo CI, Ndongo S, Meng MM, Saile R, Alibar S, Raoult D, Fournier PE. Ottowia massiliensis sp. nov., a new bacterium isolated from a fresh, healthy human fecal sample. FEMS Microbiol Lett 2022; 369:6679559. [PMID: 36044996 DOI: 10.1093/femsle/fnac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 06/24/2022] [Accepted: 08/29/2022] [Indexed: 11/12/2022] Open
Abstract
The culturomics method enabled isolation of a new member of the Ottowia genus from the stool sample of a healthy volunteer. Strain Marseille-P4747T exhibited a 96.18% 16S rRNA sequence identity with Ottowia beijingensis strain GCS-AN-3 (NR_133803.1), the closest species with standing in nomenclature. It is a Gram-stain-negative, non-motile, aerobic bacterium. It does not possess catalase and oxidase activities. Its genome has a size of 2830 447 bp and a G + C content of 63.5 mol%. Based on the phylogenic, phenotypic and genomic analyses, we conclude that Ottowia massiliensis sp. nov. is a new species, represented by Marseille-P4747T ( = CSUR P4747 = CECT 30348) as type strain.
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Affiliation(s)
- Mossaab Maaloum
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,Faculty of Sciences Ben M'sik, Laboratory of Biology and Health, Hassan II University, Casablanca, Morocco.,IHU-Méditerranée Infection, Marseille, France
| | - Cheikh Ibrahima Lo
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Sokhna Ndongo
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Marine Makoa Meng
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Rachid Saile
- Faculty of Sciences Ben M'sik, Laboratory of Biology and Health, Hassan II University, Casablanca, Morocco
| | - Stéphane Alibar
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille Univ, IRD, AP-HM, MEPHI, 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
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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Qi H, Liu D, Zou Y, Wang N, Tian H, Xiao C. Description and genomic characterization of Streptococcus symci sp. nov., isolated from a child's oropharynx. Antonie Van Leeuwenhoek 2021; 114:113-127. [PMID: 33387140 PMCID: PMC7878260 DOI: 10.1007/s10482-020-01505-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/25/2020] [Indexed: 01/01/2023]
Abstract
Using the culturomics approach, we isolated a new Streptococcus species, strain C17T, from the oropharynx mucosa sample of a healthy 5-year-old child living in Shenyang, China. We studied the phenotypic, phylogenetic, and genomic characteristics of strain C17T, which was identified as a Gram-positive, coccus-shaped, non-motile, aerobic, catalase-negative bacteria. Its growth temperatures ranged from 20 to 42 °C, with optimal growth at 37 °C. Acid production could be inhibited by two sugars, trehalose and raffinose. In C17T, the reactions for enzyme lipase (C14) were confirmed to be negative, whereas those for alkaline phosphatase, α-glucosidase, and hippuric acid hydrolysis were positive. The C17T genome contained 2,189,419 base pairs (bp), with an average G+C content of 39.95%, encoding 2092 genes in total. The 16S ribosomal RNA sequence showed 99.8% similarity with the newly identified Streptococcus pseudopneumoniae ATCC BAA-960T. The main fatty acid components in C17T were C16:0, C18:1 w7c, C18:0, and C18:1 w9c, all of which can be found in other species of the Streptococcus genus. Strain C17T showed high susceptibility to clindamycin, linezolid, vancomycin, chloramphenicol, and cefepime, and moderate susceptibility to erythromycin. The obtained dDDH value between strain C17T and the closest species was 52.9%. In addition, the whole genome sequence of strain C17T had an 82.21–93.40% average nucleotide identity (ANI) with those strains of closely related Streptococcus species, indicating that the strain C17T was unique among all Streptococcus species. Based on these characteristics, we determine that C17T is a novel species, named Streptococcus symci sp. nov. (= GDMCC 1.1633 = JCM 33582).
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Affiliation(s)
- He Qi
- Liaoning University of Traditional Chinese Medicine, Shenyang, People's Republic of China
- Department of Medical technology, Medical Science Institute of Liaoning, Shenyang, People's Republic of China
| | - Defeng Liu
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Yang Zou
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Nan Wang
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Han Tian
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China
| | - Chunling Xiao
- Key Lab of Environmental Pollution and Microecology of Liaoning Province, Shenyang Medical College, No. 146, Huanghe North Street, Shenyang, Liao Ning, People's Republic of China.
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Mbogning Fonkou MD, Lo CI, Mekhalif Z, Bilen M, Tomei E, Kuete Yimagou E, Dubourg G, Raoult D, Fenollar F, Fournier PE. Gemella massiliensis sp. nov., a new bacterium isolated from the human sputum. Arch Microbiol 2021; 203:5817-5823. [PMID: 34420080 PMCID: PMC8502168 DOI: 10.1007/s00203-021-02493-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/28/2021] [Accepted: 07/14/2021] [Indexed: 12/29/2022]
Abstract
Thanks to its ability to isolate previously uncultured bacterial species, culturomics has dynamized the study of the human microbiota. A new bacterial species, Gemella massiliensis Marseille-P3249T, was isolated from a sputum sample of a healthy French man. Strain Marseille-P3249T is a facultative anaerobe, catalase-negative, Gram positive, coccus, and unable to sporulate. The major fatty acids were C16:0 (34%), C18:1n9 (28%), C18:0 (15%) and C18:2n6 (13%). Its 16S rRNA sequence exhibits a 98.3% sequence similarity with Gemella bergeri strain 617-93T, its phylogenetically closest species with standing in nomenclature. Its digital DNA-DNA hybridization (dDDH) and OrthoANI values with G. bergeri of only 59.7 ± 5.6% and 94.8%, respectively. These values are lower than the thresholds for species delineation (> 70% and > 95%, respectively). This strain grows optimally at 37 °C and its genome is 1.80 Mbp long with a 30.5 mol% G + C content. Based on these results, we propose the creation of the new species Gemella massilienis sp. nov., strain Marseille-P3249T (= CSUR P3249 = DSMZ 103940).
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Affiliation(s)
- Maxime Descartes Mbogning Fonkou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Cheikh Ibrahima Lo
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Zouina Mekhalif
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Melhem Bilen
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
| | - Enora Tomei
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Edmond Kuete Yimagou
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Grégory Dubourg
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Florence Fenollar
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Pierre-Edouard Fournier
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.
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Kuete Yimagou E, Mekhalif F, Lamine Tall M, Baudoin JP, Raoult D, Bou Khalil JY. Prevotella marseillensis sp. nov., a new bacterium isolated from a patient with recurrent Clostridium difficile infection. New Microbes New Infect 2019; 32:100606. [PMID: 31749965 PMCID: PMC6849444 DOI: 10.1016/j.nmni.2019.100606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/02/2019] [Accepted: 09/29/2019] [Indexed: 12/22/2022] Open
Abstract
Prevotella marseillensis strain Marseille-P8229T (= CSURP8229) is a new species isolated from a patient with recurrent Clostridium difficile infection. It is an anaerobic, non-motile, non-spore-forming Gram-negative coccobacillus isolated from the stool of patient with recurrent Clostridium difficile infection in Marseille. We present herein its phenotypic description together with MALDI-TOF mass spectrometry analysis and genome sequencing and comparison. The genome of P. marseillensis is 4.1607 Mbp long with 45.80 mol% of G+C content, and it contains 3078 protein-coding genes.
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Affiliation(s)
- E Kuete Yimagou
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - F Mekhalif
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - M Lamine Tall
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - J P Baudoin
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - D Raoult
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
| | - J Y Bou Khalil
- Aix Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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Boxberger M, Anani H, La Scola B. Genome sequence and description of Alterileibacterium massiliense gen. nov., sp. nov., a new bacterium isolated from human ileum of a patient with Crohn's disease. New Microbes New Infect 2019; 30:100533. [PMID: 31198562 PMCID: PMC6556832 DOI: 10.1016/j.nmni.2019.100533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/14/2019] [Indexed: 12/22/2022] Open
Abstract
Alterileibacterium massiliense gen. nov. sp. nov. strain Marseille-P3115T (= CSURP-3115; DSM 103486), formerly proposed as Ileibacterium massiliense, is a new genus of bacteria isolated from the ileum of a human patient with Crohn's disease.
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Affiliation(s)
- M Boxberger
- Aix Marseille University, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - H Anani
- IHU-Méditerranée Infection, Marseille, France.,Aix Marseille University, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - B La Scola
- Aix Marseille University, IRD, AP-HM, MEФI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Abou Abdallah R, Cimmino T, Baron S, Cadoret F, Michelle C, Raoult D, Fournier PE, Bittar F. Description of Chryseobacterium timonianum sp. nov., isolated from a patient with pneumonia. Antonie Van Leeuwenhoek 2017; 110:1121-32. [PMID: 28509971 DOI: 10.1007/s10482-017-0885-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
Abstract
Using a polyphasic taxonomic strategy, an aerobic, Gram-negative, non-motile, yellow pigmented rod isolated from a sputum sample of a patient with pneumonia was characterised. This bacterial strain, designated G972T, could not be identified by our systematic MALDI-TOF screening on a MicroFlex. This led to the sequencing of the 16S rRNA gene, which shows 98.57% sequence identity with that of Chryseobacterium indologenes 16777T, the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. The major cell fatty acids were identified as 13-methyl-tetradecanoic acid (61%), 3-hydroxy-heptadecanoic acid (16%) and 15-methyl-11-hexadecenoic acid (11%). D-glucose, D-mannose, aesculin, D-maltose, D-trehalose, and gentibiose are the main carbon source. Digital DNA-DNA hybridization (dDDH) estimation and average nucleotide identity values (ANI) of the strain G972T against genomes of the type strains of related species ranged between 18.9 and 32.8% and between 71.46 and 83.61%, respectively, thus confirming again the new species status of the strain. Here, we describe the characteristics of this organism, complete genome sequence and annotation. The 5,390,132 bp size genome contains 4867 protein-coding genes, 89 RNAs (three genes are 5S rRNA, one gene is 16S rRNA, one gene is 23S rRNA and 84 tRNAs) with 35.51% GC content. Finally, on the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we conclude that strain strain G972T (= DSM 103388T = CSUR P2233T) represents a novel species for which we propose the name Chryseobacterium timonianum. The 16S rRNA and genome sequences are available in GenBank database under accession numbers LT161886 and FJVD00000000.
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Diop K, Diop A, Bretelle F, Cadoret F, Michelle C, Richez M, Cocallemen JF, Raoult D, Fournier PE, Fenollar F. Olegusella massiliensis gen. nov., sp. nov., strain KHD7 T, a new bacterial genus isolated from the female genital tract of a patient with bacterial vaginosis. Anaerobe 2017; 44:87-95. [PMID: 28223255 DOI: 10.1016/j.anaerobe.2017.02.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 02/02/2017] [Accepted: 02/15/2017] [Indexed: 12/13/2022]
Abstract
Strain KHD7T, a Gram-stain-positive rod-shaped, non-sporulating, strictly anaerobic bacterium, was isolated from the vaginal swab of a woman with bacterial vaginosis. We studied its phenotypic characteristics and sequenced its complete genome. The major fatty acids were C16:0 (44%), C18:2n6 (22%), and C18:1n9 (14%). The 1,806,744 bp long genome exhibited 49.24% G+C content; 1549 protein-coding and 51 RNA genes. Strain KHD7T exhibited a 93.5% 16S rRNA similarity with Olsenella uli, the phylogenetically closest species in the family Coriobacteriaceae. Therefore, strain KHD7T is sufficiently distinct to represent a new genus, for which we propose the name Olegusella massiliensis gen. nov., sp. nov. The type strain is KHD7T.
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Affiliation(s)
- Khoudia Diop
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Awa Diop
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Florence Bretelle
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France; Department of Gynecology and Obstetrics, Gynépole, Marseille, Pr Boubli et D'Ercole, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, AMU, Aix-Marseille Université, France
| | - Frédéric Cadoret
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Caroline Michelle
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Magali Richez
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Jean-François Cocallemen
- Department of Gynecology and Obstetrics, Gynépole, Marseille, Pr Boubli et D'Ercole, Hôpital Nord, Assistance Publique-Hôpitaux de Marseille, AMU, Aix-Marseille Université, France
| | - Didier Raoult
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Florence Fenollar
- Aix Marseille Univ, Institut Hospitalo-Universitaire Méditerranée-Infection, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385 Marseille Cedex 05, France.
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Tidjani Alou M, Khelaifia S, Michelle C, Andrieu C, Armstrong N, Bittar F, Sokhna C, Diallo A, Fournier PE, Raoult D, Million M. Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition. Anaerobe 2016; 40:85-94. [PMID: 27328611 DOI: 10.1016/j.anaerobe.2016.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 01/04/2023]
Abstract
Anaerococcus rubiinfantis sp. nov. strain mt16(T) is a new species within the genus Anaerococcus, which was isolated by the culturomics approach from the gut microbiota of an infant suffering from kwashiorkor. A phenotypic, biochemical and proteomic description of this strain is hereby presented alongside a complete annotation of its genome. This strictly anaerobic species forms Gram-positive non-sporeforming cocci. The major fatty acid was hexadecanoic acid. The phylogenetic analysis of strain mt16(T) showed a 97.9% similarity level with Anaerococcus vaginalis, the closest validly published species. Its genome is 1,929,161 bp long with 29.5% G + C content and contains 1808 protein-coding genes and 56 RNA genes, among which are six rRNA genes. Genomic analysis identified 41/1864 coding genes as ORFans (2.2%) and at least 620/1808 (34.9%) orthologous proteins which are not shared with the closest phylogenetic species. We believe that the extension of the human anaerobic gut compendium by culturomics is one of the first steps that will improve the understanding of the links between the microbiome and health or disease.
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Affiliation(s)
- Maryam Tidjani Alou
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Saber Khelaifia
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Caroline Michelle
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Claudia Andrieu
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Nicholas Armstrong
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Fadi Bittar
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Cheikh Sokhna
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - Aldiouma Diallo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Campus Commun UCAD-IRD of Hann, Dakar, Senegal
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France; Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Campus Commun UCAD-IRD of Hann, Dakar, Senegal; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Matthieu Million
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes IRD 198, CNRS 7278, Aix-Marseille Université, Marseille, France.
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Keita MB, Padhmanabhan R, Robert C, Delaporte E, Raoult D, Fournier PE, Bittar F. Non-contiguous-Finished Genome Sequence and Description of Paenibacillus camerounensis sp. nov. Microb Ecol 2016; 71:990-998. [PMID: 26714966 DOI: 10.1007/s00248-015-0722-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 12/15/2015] [Indexed: 06/05/2023]
Abstract
Strain G4(T) was isolated from the stool sample of a wild gorilla (Gorilla gorilla gorilla) from Cameroon. It is a facultative anaerobic, Gram-negative, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.48% with Paenibacillus typhae, the phylogenetically closest species with standing nomenclature. Moreover, the strain G4(T) presents some phenotypic differences when compared to other Paenibacillus species and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here, we describe the characteristics of this organism, complete genome sequence, and annotation. The 6,933,847 bp size genome (1 chromosome but no plasmid) contains 5972 protein-coding genes and 54 RNAs genes, including 44 tRNA genes. In addition, digital DNA-DNA hybridization values for the genome of the strain G4(T) against the closest Paenibacillus genomes range between 19.7 and 22.1, once again confirming its new status as a new species. On the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we propose the creation of Paenibacillus camerounensis sp. nov. that contains the strain G4(T).
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Affiliation(s)
| | | | - Catherine Robert
- Faculté de médecine, URMITE, Aix-Marseille Université, Marseille, France
| | | | - Didier Raoult
- Faculté de médecine, URMITE, Aix-Marseille Université, Marseille, France
- King Fahad Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | | | - Fadi Bittar
- Faculté de médecine, URMITE, Aix-Marseille Université, Marseille, France.
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Lo CI, Sankar SA, Fall B, Sambe-Ba B, Diawara S, Gueye MW, Mediannikov O, Blanc-Tailleur C, Wade B, Raoult D, Fournier PE, Fenollar F. High-quality draft genome sequence and description of Haemophilus massiliensis sp. nov. Stand Genomic Sci 2016; 11:31. [PMID: 27081435 PMCID: PMC4831113 DOI: 10.1186/s40793-016-0150-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/04/2016] [Indexed: 01/16/2023] Open
Abstract
Strain FF7T was isolated from the peritoneal fluid of a 44-year-old woman who suffered from pelvic peritonitis. This strain exhibited a 16S rRNA sequence similarity of 94.8 % 16S rRNA sequence identity with Haemophilus parasuis, the phylogenetically closest species with a name with standing in nomenclature and a poor MALDI-TOF MS score (1.32 to 1.56) that does not allow any reliable identification. Using a polyphasic study made of phenotypic and genomic analyses, strain FF7T was a Gram-negative, facultatively anaerobic rod and member of the family Pasteurellaceae. It exhibited a genome of 2,442,548 bp long genome (one chromosome but no plasmid) contains 2,319 protein-coding and 67 RNA genes, including 6 rRNA operons. On the basis of these data, we propose the creation of Haemophilus massiliensis sp. nov. with strain FF7T (= CSUR P859 = DSM 28247) as the type strain.
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Affiliation(s)
- Cheikh Ibrahima Lo
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France ; Campus international UCAD-IRD, Dakar, Senegal
| | - Senthil Alias Sankar
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
| | | | | | | | | | - Oleg Mediannikov
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France ; Campus international UCAD-IRD, Dakar, Senegal
| | - Caroline Blanc-Tailleur
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
| | | | - Didier Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France ; Campus international UCAD-IRD, Dakar, Senegal ; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France
| | - Florence Fenollar
- Aix-Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm U1095, Faculté de médecine, Marseille, France ; Campus international UCAD-IRD, Dakar, Senegal
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Sankar SA, Rathored J, Metidji S, Lagier JC, Khelaifia S, Labas N, Musso D, Raoult D, Fournier PE. Clostridium polynesiense sp. nov., a new member of the human gut microbiota in French Polynesia. Anaerobe 2015; 36:79-87. [PMID: 26485191 DOI: 10.1016/j.anaerobe.2015.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/07/2015] [Accepted: 10/10/2015] [Indexed: 11/17/2022]
Abstract
Strain MS1, a Gram-positive, obligately anaerobic, motile and spore-forming rod belonging to the Clostridium genus, was isolated from the feces of a healthy Polynesian male living in French Polynesia. The temperature range for growth was 30-45 °C. We sequenced its complete genome and studied its phenotypic characteristics. The 3,560,738-bp long genome (one chromosome, no plasmid, G + C content 34%) contained 3535 protein-coding and 70 RNA genes. Strain MS1 exhibited a 98.24% 16S rRNA similarity with Clostridium amylolyticum, the phylogenetically closest species. When compared with other Clostridium species with standing in nomenclature, it had an average genomic similarity of 68.8-70%, a unique MALDI-TOF spectrum, and differed in nitrate reduction, motility and L-arabinose and D-lactose metabolism with most of the closest species. Therefore, strain MS1 is sufficiently distinct from type strains of the genus Clostridium to represent a novel species within this genus, for which the name Clostridium polynesiense sp. nov. is proposed. The type strain of C. polynesiense is MS1(T) (= CSUR P630 = DSM 27072).
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Affiliation(s)
- Senthil Alias Sankar
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Jaishriram Rathored
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Sarah Metidji
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Saber Khelaifia
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Noemie Labas
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France
| | - Didier Musso
- Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Didier Raoult
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Faculté de médecine, 27 Boulevard Jean Moulin, 13385, Marseille Cedex 05, France.
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Merhej V, Pfleiderer A, Ramasamy D, Lagier JC, Michelle C, Raoult D, Fournier PE. Non-contiguous finished genome sequence and description of Clostridium ihumii sp. nov. Stand Genomic Sci 2015; 10:63. [PMID: 26388967 PMCID: PMC4575456 DOI: 10.1186/s40793-015-0025-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 05/21/2015] [Indexed: 12/27/2022] Open
Abstract
Clostridium ihumii strain AP5T sp. nov. is a new species within the genus Clostridium. This strain, whose genome is described here, was isolated from the stool sample of a 21-year-old French Caucasian female with anorexia nervosa. C. ihumii is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,433,668 bp long genome contains 4,076 protein-coding and 85 RNA genes, including 9 rRNA genes.
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Affiliation(s)
- Vicky Merhej
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, cedex 05 France
| | - Anne Pfleiderer
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, cedex 05 France
| | - Dhamodharan Ramasamy
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, cedex 05 France
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, cedex 05 France
| | - Caroline Michelle
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, cedex 05 France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, cedex 05 France
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM 63, CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, 27 Boulevard Jean Moulin, 13385, Marseille, cedex 05 France
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Bittar F, Bibi F, Ramasamy D, Lagier JC, Azhar EI, Jiman-Fatani AA, Al-Ghamdi AK, Nguyen TT, Yasir M, Fournier PE, Raoult D. Non contiguous-finished genome sequence and description of Bacillus jeddahensis sp. nov. Stand Genomic Sci 2015; 10:47. [PMID: 26380635 DOI: 10.1186/s40793-015-0024-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 05/21/2015] [Indexed: 11/13/2022] Open
Abstract
Strain JCET was isolated from the fecal sample of a 24-year-old obese man living in Jeddah, Saudi Arabia. It is an aerobic, Gram-positive, rod-shaped bacterium. This strain exhibits a 16S rRNA nucleotide sequence similarity of 97.5 % with Bacillus niacini, the phylogenetically closest species with standing nomenclature. Moreover, the strain JCET presents many phenotypic differences, when it is compared to other Bacillus species, and shows a low MALDI-TOF Mass Spectrometry score that does not allow any identification. Thus, it is likely that this strain represents a new species. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,762,944 bp long genome (1 chromosome but no plasmid) contains 4,654 protein-coding and 98 RNAs genes, including 92 tRNA genes. The strain JCET differs from most of the other closely Bacillus species by more than 1 % in G + C content. In addition, digital DNA-DNA hybridization values for the genome of the strain JCET against the closest Bacillus genomes range between 19.5 to 28.1, that confirming again its new species status. On the basis of these polyphasic data made of phenotypic and genomic analyses, we propose the creation of Bacillus jeddahensis sp. nov. that contains the strain JCET.
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Angelakis E, Bibi F, Ramasamy D, Azhar EI, Jiman-Fatani AA, Aboushoushah SM, Lagier JC, Robert C, Caputo A, Yasir M, Fournier PE, Raoult D. Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov. Stand Genomic Sci 2014; 9:8. [PMID: 25780501 PMCID: PMC4334108 DOI: 10.1186/1944-3277-9-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 12/03/2022] Open
Abstract
Clostridium saudii strain JCC(T) sp. nov. is the type strain of C. saudii sp. nov., a new species within the genus Clostridia. This strain, whose genome is described here, was isolated from a fecal sample collected from an obese 24-year-old (body mass index 52 kg/m2) man living in Jeddah, Saudi Arabia. C. saudii is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,653,762 bp long genome contains 3,452 protein-coding and 53 RNA genes, including 4 rRNA genes.
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Affiliation(s)
- Emmanouil Angelakis
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Dhamodharan Ramasamy
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Asif A Jiman-Fatani
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sally M Aboushoushah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Catherine Robert
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Aurelia Caputo
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS, Institut Hospitalo-Universitaire Méditerranée-Infection, Faculté de médecine, Aix-Marseille Université, Marseille, France
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
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Ramasamy D, Lagier JC, Nguyen TT, Raoult D, Fournier PE. Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae. Stand Genomic Sci 2013; 8:336-51. [PMID: 23991263 PMCID: PMC3746426 DOI: 10.4056/sigs.3567059] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Dielma fastidiosa strain JC13(T) gen. nov., sp. nov. is the type strain of D. fastidiosa gen. nov., sp. nov., the type species of a new genus within the family Erysipelotrichaceae. This strain, whose draft genome is described here, was isolated from the fecal flora of a healthy 16-year-old male Senegalese volunteer. D. fastidiosa is a Gram-negative anaerobic rod. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,574,031 bp long genome comprises a 3,556,241-bp chromosome and a 17,790-bp plasmid. The chromosome contains 3,441 protein-coding and 50 RNA genes, including 3 rRNA genes, whereas the plasmid contains 17 protein-coding genes.
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Affiliation(s)
| | | | - Thi Tien Nguyen
- Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, URMITE, Faculté de médecine, Marseille, France
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