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Advanced prokaryotic systematics: the modern face of an ancient science. New Microbes New Infect 2022; 49-50:101036. [DOI: 10.1016/j.nmni.2022.101036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
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Mohd Salleh MH, Esa Y, Ngalimat MS, Chen PN. Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis. PeerJ 2022; 10:e12970. [PMID: 35368336 PMCID: PMC8973471 DOI: 10.7717/peerj.12970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/30/2022] [Indexed: 01/11/2023] Open
Abstract
Southern River Terrapin, Batagur affinis, is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can shield light on the host-associated microbial communities that play important roles in host health. Thus, this study aimed to characterise and compare the faecal bacterial community between captive and wild B. affinis using metabarcoding approaches. A total of seven faeces samples were collected from captive (N = 5) and wild (N = 2) adult B. affinis aseptically, crossing the East and West coast of peninsular Malaysia. The DNA was extracted from the faeces samples, and the 16S rRNA gene (V3-V4 region) was amplified using polymerase chain reaction (PCR). The amplicon was further analysed using SILVA and DADA2 pipelines. In total, 297 bacterial communities taxonomic profile (phylum to genus) were determined. Three phyla were found in high abundance in all faeces samples, namely Firmicutes (38.69%), Bacteroidetes (24.52%), and Fusobacteria (6.95%). Proteobacteria were detected in all faeces samples (39.63%), except the wild sample, KBW3. Under genus level, Cetobacteriumwas found as the most abundant genus (67.79%), followed by Bacteroides (24.56%) and Parabacteroides (21.78%). The uncultured genus had the highest abundance (88.51%) even though not detected in the BK31 and KBW2 samples. The potential probiotic genera (75.00%) were discovered to be more dominant in B. affinis faeces samples. Results demonstrated that the captive B. affinis faeces samples have a greater bacterial variety and richness than wild B. affinis faeces samples. This study has established a starting point for future investigation of the gut microbiota of B. affinis.
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Affiliation(s)
- Mohd Hairul Mohd Salleh
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia,Royal Malaysian Customs Department, Presint 2, Putrajaya, Malaysia
| | - Yuzine Esa
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia,International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Port Dickson, Negeri Sembilan, Malaysia
| | - Mohamad Syazwan Ngalimat
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Pelf Nyok Chen
- Turtle Conservation Society of Malaysia, Kemaman, Terengganu, Malaysia
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Ezeji JC, Sarikonda DK, Hopperton A, Erkkila HL, Cohen DE, Martinez SP, Cominelli F, Kuwahara T, Dichosa AEK, Good CE, Jacobs MR, Khoretonenko M, Veloo A, Rodriguez-Palacios A. Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health. Gut Microbes 2022; 13:1922241. [PMID: 34196581 PMCID: PMC8253142 DOI: 10.1080/19490976.2021.1922241] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Parabacteroides distasonis is the type strain for the genus Parabacteroides, a group of gram-negative anaerobic bacteria that commonly colonize the gastrointestinal tract of numerous species. First isolated in the 1930s from a clinical specimen as Bacteroides distasonis, the strain was re-classified to form the new genus Parabacteroides in 2006. Currently, the genus consists of 15 species, 10 of which are listed as 'validly named' (P. acidifaciens, P. chartae, P. chinchillae, P. chongii, P. distasonis, P. faecis, P. goldsteinii, P. gordonii, P. johnsonii, and P. merdae) and 5 'not validly named' (P. bouchesdurhonensis, P. massiliensis, P. pacaensis, P. provencensis, and P. timonensis) by the List of Prokaryotic names with Standing in Nomenclature. The Parabacteroides genus has been associated with reports of both beneficial and pathogenic effects in human health. Herein, we review the literature on the history, ecology, diseases, antimicrobial resistance, and genetics of this bacterium, illustrating the effects of P. distasonis on human and animal health.
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Affiliation(s)
- Jessica C. Ezeji
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Daven K. Sarikonda
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Austin Hopperton
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio, USA
| | - Hailey L. Erkkila
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Daniel E. Cohen
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | | | - Fabio Cominelli
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA,Germ-Free and Gut Microbiome Core, Case Western Reserve University, Cleveland, OH, United States
| | - Tomomi Kuwahara
- Department of Microbiology, Faculty of Medicine, Kagawa University, Miki, Kagawa, Japan
| | - Armand E. K. Dichosa
- B-10 Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Caryn E. Good
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Michael R. Jacobs
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | | | - Alida Veloo
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alexander Rodriguez-Palacios
- Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA,Germ-Free and Gut Microbiome Core, Case Western Reserve University, Cleveland, OH, United States,University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA,CONTACT Alexander Rodriguez-Palacios Digestive Diseases Research Institute, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Lo CI, Dione N, Mbaye A, Gómez PFM, Ngom II, Valles C, Alibar S, Lagier JC, Fenollar F, Fournier PE, Raoult D, Diene SM. Limosilactobacillus caccae sp. nov., a new bacterial species isolated from the human gut microbiota. FEMS Microbiol Lett 2021; 368:6373442. [PMID: 34549292 DOI: 10.1093/femsle/fnab128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/17/2021] [Indexed: 11/14/2022] Open
Abstract
Strain Marseille-P3519T isolated from the fecal flora of a 25-year-old healthy French woman was a Gram-positive anaerobic bacterium, non-motile and non-spore forming. The 16S rRNA gene sequence of Marseille-P3519 showed 97.73% of sequence similarity with Limosilactobacillus reuteri DSM 20016, the closest species, phylogenetically. Furthermore, the average nucleotide identity of strain Marseille-3519 with its closest related species was 75.8% that was very below the recommended threshold (>95-96%). Its genome had 2 237 367 bp with 45.42 mol% of G + C content. Major fatty acids were C16:0 (50.8%), C18:1n9 (18.0%), C18:2n6 (9.8%) and C19:1n9 (8.9%). It was catalase negative and fermented glycerol, glucose, fructose, D-maltose, lactose and mannose. These findings support that strain Marseille-P3519 ( = CSURP3519 = CECT 30110) is a new member of the genus Limosilactobacillus for which the name Limosilactobacillus caccae sp. nov., is proposed.
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Affiliation(s)
- Cheikh Ibrahima Lo
- Aix Marseille Uni versity, IRD, AP-HM, SSA, VITROME, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Niokhor Dione
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Aminata Mbaye
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Patricia Fernández-Mellado Gómez
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Issa Isaac Ngom
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Camille Valles
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Stéphane Alibar
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Jean-Christophe Lagier
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Florence Fenollar
- Aix Marseille Uni versity, IRD, AP-HM, SSA, VITROME, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Pierre-Edouard Fournier
- Aix Marseille Uni versity, IRD, AP-HM, SSA, VITROME, Marseille, France.,Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
| | - Seydina M Diene
- Institut Hospitalo-Universitaire Méditerranée-Infection, 19-21 Boulevard Jean Moulin, 13385, Marseille cedex 05, France.,Aix Marseille University , IRD, AP-HM, MEPHI, Marseille, France
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Khare M, Sinha D, Zgheib R, Traore SI, Lagier JC, Raoult D, Edouard FP. Genomic description and characterization of Nigeribacterium massiliense gen. nov., sp. nov., isolated from the human gut. Microbes Infect 2021; 23:104842. [PMID: 34020025 DOI: 10.1016/j.micinf.2021.104842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/23/2021] [Accepted: 05/08/2021] [Indexed: 02/07/2023]
Abstract
Strain Marseille-P1302 was isolated from the stool of a 2-year-old Nigerian boy suffering from Kwashiorkor, a form of severe acute malnutrition. The strain grows in aerobic atmosphere and bacterial cells are Gram-positive cocci ranging in diameter from 0.8 to 1 μm. Strain Marseille-P1302 exhibits a 16S rRNA sequence similarity of 94.97% with Brevilactibacter flavus strain VG341T, but phylogenetically-closest species with standing in nomenclature is Brevilactibacter sinopodophylli strains KCTC 33808Twith the sequence similarity of 93.41%. The draft genome of strain Marseille-P1302 is 2,934,258bp-long with a 70.38% G+C content, and contains 2,704 protein-coding genes and 55 RNAs that includes 9 rRNA genes. On the basis of these data, we propose the creation of the new genus Nigeribacterium gen. nov., with strain Marseille-P1302T (= CSUR P1302 = DSM 29084) being the type strain of new species Nigeribacterium. massiliense gen. nov., sp. nov.
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Affiliation(s)
- Mudra Khare
- Aix Marseille University, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, UMR Vecteurs Infections Tropicales et Méditerranéennes. (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Dhiraj Sinha
- Aix Marseille University, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, UMR Vecteurs Infections Tropicales et Méditerranéennes. (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Rita Zgheib
- Aix Marseille University, Institut de Recherche pour le Développement (IRD), Service de Santé des Armées, Assistance Publique-Hôpitaux de Marseille, UMR Vecteurs Infections Tropicales et Méditerranéennes. (VITROME), Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France; Institut Méditerranée-Infection, Marseille, France
| | - Sory Ibrahima Traore
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Jean-Christophe Lagier
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Fournier Pierre Edouard
- Institut Méditerranée-Infection, Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Dévelopement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France.
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Microbial community composition and its role in volatile compound formation during the spontaneous fermentation of ice wine made from Vidal grapes. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.01.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Bilen M, Mbogning Fonkou MD, Khelaifia S, Tomei E, Cadoret F, Daoud Z, Armstrong N, Bittar F, Fournier PE, Raoult D, Dubourg G. Taxonogenomics description of Parabacteroides timonensis sp. nov. isolated from a human stool sample. Microbiologyopen 2018; 8:e00702. [PMID: 30311407 PMCID: PMC6460270 DOI: 10.1002/mbo3.702] [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: 04/02/2018] [Revised: 06/29/2018] [Accepted: 07/02/2018] [Indexed: 01/02/2023] Open
Abstract
Intensive efforts have been made to describe the human microbiome and its involvement in health and disease. Culturomics has been recently adapted to target formerly uncultured bacteria and other unclassified bacterial species. This approach enabled us to isolate in the current study a new bacterial species, Parabacteroides timonensis strain Marseille‐P3236T, from a stool sample of a healthy 39‐year‐old pygmy male. This strain, is an anaerobic, gram‐negative, nonspore‐forming motile rod. Its genome is made up of 6,483,434 bp with 43.41% G+C content, 5046 protein‐encoding genes, and 84 RNA genes. We herein provide the full description of Parabacteroides timonensis strain Marseille‐P3236T through the taxonogenomic approach.
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Affiliation(s)
- Melhem Bilen
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU Méditerranée-Infection, Marseille, France.,Clinical Microbiology Department, Faculty of Medicine and Medical sciences, University of Balamand, Amioun, Lebanon
| | | | - Saber Khelaifia
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - Enora Tomei
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - Frédéric Cadoret
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - Ziad Daoud
- Aix Marseille University, IRD, AP-HM, SSA, VITROME, IHU Méditerranée-Infection, Marseille, France
| | - Nicholas Armstrong
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | - Fadi Bittar
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU Méditerranée-Infection, Marseille, France
| | | | - Didier Raoult
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU Méditerranée-Infection, Marseille, France.,Assistance Publique Hôpitaux de Marseille (AP-HM), IHU Méditerranée-Infection, Marseille, France.,Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Gregory Dubourg
- Aix Marseille University, IRD, AP-HM, MEPHI, IHU Méditerranée-Infection, Marseille, France
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