1
|
Arahal DR, Bull CT, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Ventosa A, Young P, Göker M. Judicial Opinion 129. Int J Syst Evol Microbiol 2024; 74. [PMID: 38376502 DOI: 10.1099/ijsem.0.006064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
Opinion 129 addresses the status of Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980). The name has the category 'division' and was included in the Approved Lists of Bacterial Names, although that category had previously been removed from the International Code of Nomenclature of Bacteria (1975 revision onwards). When the category 'phylum' was introduced into the International Code of Nomenclature of Prokaryotes (ICNP) in 2021, equivalence between 'phylum' and 'division' was not stipulated. Since the definition of the taxonomic categories and their relative order is one of the principal tasks of every code of nomenclature, the inclusion of Firmicutes corrig. Gibbons and Murray 1978 in the Approved Lists was an error. The name is either not validly published or illegitimate because its category is not covered by the ICNP. If Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980) was a validly published phylum name, it would be illegitimate because it would contravene Rule 8, which does not permit any deviation from the requirement to derive a phylum name from the name of the type genus. Since Firmicutes corrig. Gibbons and Murray 1978 is also part of a 'misfitting megaclassification' recognized in Opinion 128, the name is rejected, without any pre-emption regarding a hypothetically validly published name Firmicutes at the rank of phylum. Gracilicutes Gibbons and Murray 1978 (Approved Lists 1980) and Anoxyphotobacteriae Gibbons and Murray 1978 (Approved Lists 1980) are also rejected. The validly published phylum names have a variety of advantages over their not validly published counterparts and cannot be replaced with ad hoc names suggested in the literature. To ease the transition, it is recommended to mention the not validly published phylum names which strongly deviate in spelling from their validly published counterparts along with the latter in publications during the next years.
Collapse
Affiliation(s)
- David R Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, PA 16802, USA
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Maria Chuvochina
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, QLD 4072, Australia
| | - Svetlana N Dedysh
- Research Center of Biotechnology RAS, Winogradsky Institute of Microbiology, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | | | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Charles T Parker
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, C/. Prof. Garcia Gonzalez 2, ES-41012 Sevilla, Spain
| | - Peter Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| |
Collapse
|
2
|
Xie F, Zhao S, Zhan X, Zhou Y, Li Y, Zhu W, Pope PB, Attwood GT, Jin W, Mao S. Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions. Genome Biol 2024; 25:32. [PMID: 38263062 PMCID: PMC10804542 DOI: 10.1186/s13059-024-03167-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 01/07/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are defined via a limited number of cultured strains. RESULTS Here, we profile and analyze 243 Methanomassiliicoccales genomes assembled from cultured representatives and uncultured metagenomes recovered from various biomes, including the gastrointestinal tracts of different animal species. Our analyses reveal the presence of numerous undefined genera and genetic variability in metabolic capabilities within Methanomassiliicoccales lineages, which is essential for adaptation to their ecological niches. In particular, gastrointestinal tract Methanomassiliicoccales demonstrate the presence of co-diversified members with their hosts over evolutionary timescales and likely originated in the natural environment. We highlight the presence of diverse clades of vitamin transporter BtuC proteins that distinguish Methanomassiliicoccales from other archaeal orders and likely provide a competitive advantage in efficiently handling B12. Furthermore, genome-centric metatranscriptomic analysis of ruminants with varying methane yields reveal elevated expression of select Methanomassiliicoccales genera in low methane animals and suggest that B12 exchanges could enable them to occupy ecological niches that possibly alter the direction of H2 utilization. CONCLUSIONS We provide a comprehensive and updated account of divergent Methanomassiliicoccales lineages, drawing from numerous uncultured genomes obtained from various habitats. We also highlight their unique metabolic capabilities involving B12, which could serve as promising targets for mitigating ruminant methane emissions by altering H2 flow.
Collapse
Affiliation(s)
- Fei Xie
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Shengwei Zhao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoxiu Zhan
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yang Zhou
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yin Li
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Phillip B Pope
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Graeme T Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Wei Jin
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
| |
Collapse
|
3
|
Liu Y, Du J, Zhang J, Lai Q, Shao Z, Zhu H. Parahaliea maris sp. nov., isolated from surface seawater and emended description of the genus Parahaliea. J Microbiol 2020; 58:92-98. [DOI: 10.1007/s12275-020-9405-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/28/2019] [Accepted: 12/02/2019] [Indexed: 01/07/2023]
|
4
|
Watanabe M, Kojima H, Fukui M. Labilibaculum antarcticum sp. nov., a novel facultative anaerobic, psychrotorelant bacterium isolated from marine sediment of Antarctica. Antonie Van Leeuwenhoek 2019; 113:349-355. [PMID: 31628625 DOI: 10.1007/s10482-019-01345-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/02/2019] [Indexed: 11/26/2022]
Abstract
A novel facultative anaerobic and facultative psychrophilic bacterium, designated SPP2T, was isolated from an Antarctic marine sediment. Cells of the isolate were observed to be long rods (0.5 × 5-10 μm), Gram-stain negative and to have gliding motility. For growth, the optimum NaCl concentration was found to be 2-3% and the optimum temperature to be 18-22 °C. Strain SPP2T cannot use sulfate and nitrate as electron acceptors in the presence of lactate. The G+C content of the genomic DNA was determined to be 36.0 mol%.. The major cellular fatty acids were identified as anteiso-C15:0 and iso-C15:0. MK-7 was found to be the predominant respiratory quinone. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belongs to the family Marinifilaceae and to be closely related to Labilibaculum manganireducens 59.10-2MT with 16S rRNA gene sequence identity of 98%. The OrthoANI and dDDH values between the genome sequences of strain SPP2T and its close relative were 84% and 27.3%, which are lower than the threshold values for species delineation. On the basis of phylogenetic and phenotypic characterisation, Labilibaculum antarcticum sp. nov. is proposed with the type strain SPP2T (= NBRC 111151T = CECT 9460T).
Collapse
Affiliation(s)
- Miho Watanabe
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan.
- Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo, 102-8471, Japan.
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Hisaya Kojima
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
| | - Manabu Fukui
- The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060-0819, Japan
| |
Collapse
|
5
|
The status of names whose nomenclatural types are based on strains deposited solely for patent purposes. Int J Syst Evol Microbiol 2019; 69:2616-2620. [DOI: 10.1099/ijsem.0.003527] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
6
|
El Houari A, Ranchou-Peyruse M, Ranchou-Peyruse A, Dakdaki A, Guignard M, Idouhammou L, Bennisse R, Bouterfass R, Guyoneaud R, Qatibi AI. Desulfobulbus oligotrophicus sp. nov., a sulfate-reducing and propionate-oxidizing bacterium isolated from a municipal anaerobic sewage sludge digester. Int J Syst Evol Microbiol 2017; 67:275-281. [DOI: 10.1099/ijsem.0.001615] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Abdelaziz El Houari
- Université de Pau et des Pays de l’Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, 64013 Pau, France
- Anaerobic Microbiology Team (E02B26), Sciences and Techniques Faculty, Cadi Ayyad University PO Box 549, 40 000 Marrakech, Morocco
| | - Magali Ranchou-Peyruse
- Université de Pau et des Pays de l’Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, 64013 Pau, France
| | - Anthony Ranchou-Peyruse
- Université de Pau et des Pays de l’Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, 64013 Pau, France
| | - Adrien Dakdaki
- Université de Pau et des Pays de l’Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, 64013 Pau, France
| | - Marion Guignard
- Université de Pau et des Pays de l’Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, 64013 Pau, France
| | - Lahcen Idouhammou
- Anaerobic Microbiology Team (E02B26), Sciences and Techniques Faculty, Cadi Ayyad University PO Box 549, 40 000 Marrakech, Morocco
| | - Rhizlane Bennisse
- Anaerobic Microbiology Team (E02B26), Sciences and Techniques Faculty, Cadi Ayyad University PO Box 549, 40 000 Marrakech, Morocco
| | - Radia Bouterfass
- Anaerobic Microbiology Team (E02B26), Sciences and Techniques Faculty, Cadi Ayyad University PO Box 549, 40 000 Marrakech, Morocco
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l’Adour, CNRS, IPREM UMR 5254, Equipe Environnement et Microbiologie, 64013 Pau, France
| | - Abdel-Illah Qatibi
- Anaerobic Microbiology Team (E02B26), Sciences and Techniques Faculty, Cadi Ayyad University PO Box 549, 40 000 Marrakech, Morocco
| |
Collapse
|
7
|
Fournier PE, Lagier JC, Dubourg G, Raoult D. From culturomics to taxonomogenomics: A need to change the taxonomy of prokaryotes in clinical microbiology. Anaerobe 2015; 36:73-8. [DOI: 10.1016/j.anaerobe.2015.10.011] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 10/06/2015] [Accepted: 10/23/2015] [Indexed: 01/07/2023]
|
8
|
Uchino Y, Miura T, Hosoyama A, Ohji S, Yamazoe A, Ito M, Takahata Y, Suzuki KI, Fujita N. Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method. Stand Genomic Sci 2015; 10:102. [PMID: 26568785 PMCID: PMC4644273 DOI: 10.1186/s40793-015-0095-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 11/02/2015] [Indexed: 11/10/2022] Open
Abstract
A novel Dehalococcoides sp. strain UCH007 was isolated from the groundwater polluted with chlorinated ethenes in Japan. This strain is capable of dechlorinating trichloroethene, cis-1,2-dichloroethene and vinyl chloride to ethene. Dehalococcoides bacteria are hardly cultivable, so genome sequencing has presented a challenge. In this study, we developed a differential reads picking method for mixed genomic DNA obtained from a co-culture, and applied it to the sequencing of strain UCH007. The genome of strain UCH007 consists of a 1,473,548-bp chromosome that encodes 1509 coding sequences including 29 putative reductive dehalogenase genes. Strain UCH007 is the first strain in the Victoria subgroup found to possess the pceA, tceA and vcrA genes.
Collapse
Affiliation(s)
- Yoshihito Uchino
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| | - Takamasa Miura
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| | - Akira Hosoyama
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| | - Shoko Ohji
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| | - Atsushi Yamazoe
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| | - Masako Ito
- />Taisei Corporation, 344-1 Nase, Kanagawa, 245-0051 Japan
| | - Yoh Takahata
- />Taisei Corporation, 344-1 Nase, Kanagawa, 245-0051 Japan
| | - Ken-ichiro Suzuki
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| | - Nobuyuki Fujita
- />Biological Resource Center, National Institute of Technology and Evaluation, 2-10-49 Nishihara, Tokyo, 151-0066 Japan
| |
Collapse
|
9
|
Sankar SA, Rathored J, Metidji S, Lagier JC, Khelaifia S, Labas N, Musso D, Raoult D, Fournier PE. Clostridium polynesiense sp. nov., a new member of the human gut microbiota in French Polynesia. Anaerobe 2015; 36:79-87. [PMID: 26485191 DOI: 10.1016/j.anaerobe.2015.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/07/2015] [Accepted: 10/10/2015] [Indexed: 11/17/2022]
Abstract
Strain MS1, a Gram-positive, obligately anaerobic, motile and spore-forming rod belonging to the Clostridium genus, was isolated from the feces of a healthy Polynesian male living in French Polynesia. The temperature range for growth was 30-45 °C. We sequenced its complete genome and studied its phenotypic characteristics. The 3,560,738-bp long genome (one chromosome, no plasmid, G + C content 34%) contained 3535 protein-coding and 70 RNA genes. Strain MS1 exhibited a 98.24% 16S rRNA similarity with Clostridium amylolyticum, the phylogenetically closest species. When compared with other Clostridium species with standing in nomenclature, it had an average genomic similarity of 68.8-70%, a unique MALDI-TOF spectrum, and differed in nitrate reduction, motility and L-arabinose and D-lactose metabolism with most of the closest species. Therefore, strain MS1 is sufficiently distinct from type strains of the genus Clostridium to represent a novel species within this genus, for which the name Clostridium polynesiense sp. nov. is proposed. The type strain of C. polynesiense is MS1(T) (= CSUR P630 = DSM 27072).
Collapse
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.
| |
Collapse
|
10
|
Ramasamy D, Mishra AK, Lagier JC, Padhmanabhan R, Rossi M, Sentausa E, Raoult D, Fournier PE. A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species. Int J Syst Evol Microbiol 2014; 64:384-391. [DOI: 10.1099/ijs.0.057091-0] [Citation(s) in RCA: 306] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Currently, bacterial taxonomy relies on a polyphasic approach based on the combination of phenotypic and genotypic characteristics. However, the current situation is paradoxical in that the genetic criteria that are used, including DNA–DNA hybridization, 16S rRNA gene sequence nucleotide similarity and phylogeny, and DNA G+C content, have significant limitations, but genome sequences that contain the whole genetic information of bacterial strains are not used for taxonomic purposes, despite the decreasing costs of sequencing and the increasing number of available genomes. Recently, we diversified bacterial culture conditions with the aim of isolating uncultivated bacteria. To classify the putative novel species that we cultivated, we used a polyphasic strategy that included phenotypic as well as genomic criteria (genome characteristics as well as genomic sequence similarity). Herein, we review the pros and cons of genome sequencing for taxonomy and propose that the incorporation of genome sequences in taxonomic studies has the advantage of using reliable and reproducible data. This strategy, which we name taxono-genomics, may contribute to the taxonomic classification of bacteria.
Collapse
Affiliation(s)
- Dhamodharan Ramasamy
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Ajay Kumar Mishra
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Jean-Christophe Lagier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Roshan Padhmanabhan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Morgane Rossi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Erwin Sentausa
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes URMITE, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, UMR63, CNRS 7278, IRD 198, INSERM U1095, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| |
Collapse
|