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Sutcliffe I, Rosselló-Móra R, Trujillo M. Addressing the sublime scale of the microbial world: reconciling an appreciation of microbial diversity with the need to describe species. New Microbes New Infect 2021; 43:100931. [PMID: 34484799 PMCID: PMC8408622 DOI: 10.1016/j.nmni.2021.100931] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/07/2021] [Accepted: 08/03/2021] [Indexed: 12/22/2022] Open
Abstract
There are fewer than 20,000 prokaryotic species with validly published names, meaning >99% of a reasonable estimate of microbial diversity remains formally unnamed. Here we explore the damaging consequences of the current practice in which each new species is described in a standardized publication, most typically a 'single strain species description'. This approach is both an impediment to scaling up progress in naming the microbial world and also a significant factor in the poor reputation of the discipline of microbial taxonomy. We conclude that significant changes in author habits are needed and make constructive suggestions as to how author practice should adapt.
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Affiliation(s)
- I.C. Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - R. Rosselló-Móra
- Grup de Microbiologia Marina, IMEDEA (CSIC-UIB), C/Miquel Marques 21, 07190, Esporles, Illes Balears, Spain
| | - M.E. Trujillo
- Dpto. Microbiología y Genética, University of Salamanca, 37007, Salamanca, Spain
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Munson E, Carroll KC. An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017. J Clin Microbiol 2019; 57:e01181-18. [PMID: 30257907 PMCID: PMC6355528 DOI: 10.1128/jcm.01181-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and Evolutionary Microbiology Noteworthy discussion centers around descriptions of novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Borrelia, and Enterobacter genera; and a major reorganization of the family Enterobacteriaceae. JCM intends to sustain this series of reports as advancements in molecular genetics, whole-genome sequencing, and studies of the human microbiome continue to produce novel taxa and clearer understandings of bacterial relatedness.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Gupta RS, Lo B, Son J. Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera. Front Microbiol 2018; 9:67. [PMID: 29497402 PMCID: PMC5819568 DOI: 10.3389/fmicb.2018.00067] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023] Open
Abstract
The genus Mycobacterium contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of Mycobacterium species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus Mycobacterium, 136 core proteins for the phylum Actinobacteria and 8 other conserved proteins. Additionally, the overall genome similarity amongst the Mycobacterium species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus Mycobacterium at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all Mycobacterium species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus Mycobacterium and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus Mycobacterium into an emended genus Mycobacterium encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. Mycolicibacterium gen. nov., Mycolicibacter gen. nov., Mycolicibacillus gen. nov. and Mycobacteroides gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.
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Affiliation(s)
- Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, CA, Canada
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Beukes CW, Palmer M, Manyaka P, Chan WY, Avontuur JR, van Zyl E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Daum C, Shapiro N, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Blom J, Whitman WB, Venter SN, Steenkamp ET. Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato. Front Microbiol 2017; 8:1154. [PMID: 28694797 PMCID: PMC5483467 DOI: 10.3389/fmicb.2017.01154] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/07/2017] [Indexed: 12/21/2022] Open
Abstract
Although the taxonomy of Burkholderia has been extensively scrutinized, significant uncertainty remains regarding the generic boundaries and composition of this large and heterogeneous taxon. Here we used the amino acid and nucleotide sequences of 106 conserved proteins from 92 species to infer robust maximum likelihood phylogenies with which to investigate the generic structure of Burkholderia sensu lato. These data unambiguously supported five distinct lineages, of which four correspond to Burkholderia sensu stricto and the newly introduced genera Paraburkholderia, Caballeronia, and Robbsia. The fifth lineage was represented by P. rhizoxinica. Based on these findings, we propose 13 new combinations for those species previously described as members of Burkholderia but that form part of Caballeronia. These findings also suggest revision of the taxonomic status of P. rhizoxinica as it is does not form part of any of the genera currently recognized in Burkholderia sensu lato. From a phylogenetic point of view, Burkholderia sensu stricto has a sister relationship with the Caballeronia+Paraburkholderia clade. Also, the lineages represented by P. rhizoxinica and R. andropogonis, respectively, emerged prior to the radiation of the Burkholderia sensu stricto+Caballeronia+Paraburkholderia clade. Our findings therefore constitute a solid framework, not only for supporting current and future taxonomic decisions, but also for studying the evolution of this assemblage of medically, industrially and agriculturally important species.
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Affiliation(s)
- Chrizelle W Beukes
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Puseletso Manyaka
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Wai Y Chan
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Juanita R Avontuur
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Elritha van Zyl
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | | | - Alicia Clum
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Manoj Pillay
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | | | - Neha Varghese
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | | | | | - T B K Reddy
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Chris Daum
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | | | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut CreekCA, United States
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University GiessenGiessen, Germany
| | - William B Whitman
- Department of Microbiology, University of Georgia, AthensGA, United States
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
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