A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index
Abstract
Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in themore »
- Authors:
-
[2];
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
- Publication Date:
- Research Org.:
- NamesforLife, LLC, East Lansing, MI (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Science Foundation (NSF); Gordon and Betty Moore Foundation; Smithsonian Tropical Research Institute; Center for Dark Energy Biosphere Investigations
- OSTI Identifier:
- 1582484
- Alternate Identifier(s):
- OSTI ID: 1626150
- Grant/Contract Number:
- FG02-07ER86321; SC0006191; 1523639; GBMF5603; OCE-039564
- Resource Type:
- Published Article
- Journal Name:
- mBio
- Additional Journal Information:
- Journal Name: mBio Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 2161-2129
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; microbiology; ANI; Bacillus; Clostridium; Lactobacillus; Photorhabdus; Pseudomonas; Xenorhabdus; delineation; demarcation; genus; systematics; taxonomy
Citation Formats
Barco, R. A., Garrity, G. M., Scott, J. J., Amend, J. P., Nealson, K. H., Emerson, D., and Giovannoni, ed., Stephen J. A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index. United States: N. p., 2020.
Web. doi:10.1128/mBio.02475-19.
Barco, R. A., Garrity, G. M., Scott, J. J., Amend, J. P., Nealson, K. H., Emerson, D., & Giovannoni, ed., Stephen J. A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index. United States. https://doi.org/10.1128/mBio.02475-19
Barco, R. A., Garrity, G. M., Scott, J. J., Amend, J. P., Nealson, K. H., Emerson, D., and Giovannoni, ed., Stephen J. Tue .
"A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index". United States. https://doi.org/10.1128/mBio.02475-19.
@article{osti_1582484,
title = {A Genus Definition for Bacteria and Archaea Based on a Standard Genome Relatedness Index},
author = {Barco, R. A. and Garrity, G. M. and Scott, J. J. and Amend, J. P. and Nealson, K. H. and Emerson, D. and Giovannoni, ed., Stephen J.},
abstractNote = {Genus assignment is fundamental in the characterization of microbes, yet there is currently no unambiguous way to demarcate genera solely using standard genomic relatedness indices. Here, we propose an approach to demarcate genera that relies on the combined use of the average nucleotide identity, genome alignment fraction, and the distinction between type- and non-type species. More than 3,500 genomes representing type strains of species from >850 genera of either bacterial or archaeal lineages were tested. Over 140 genera were analyzed in detail within the taxonomic context of order/family. Significant genomic differences between members of a genus and type species of other genera in the same order/family were conserved in 94% of the cases. Nearly 90% (92% if polyphyletic genera are excluded) of the type strains were classified in agreement with current taxonomy. The 448 type strains that need reclassification directly impact 33% of the genera analyzed in detail. The results provide a first line of evidence that the combination of genomic indices provides added resolution to effectively demarcate genera within the taxonomic framework that is currently based on the 16S rRNA gene. We also identify the emergence of natural breakpoints at the genome level that can further help in the circumscription of taxa, increasing the proportion of directly impacted genera to at least 43% and pointing at inaccuracies on the use of the 16S rRNA gene as a taxonomic marker, despite its precision. Altogether, these results suggest that genomic coherence is an emergent property of genera in Bacteria and Archaea.},
doi = {10.1128/mBio.02475-19},
journal = {mBio},
number = 1,
volume = 11,
place = {United States},
year = {Tue Feb 25 00:00:00 EST 2020},
month = {Tue Feb 25 00:00:00 EST 2020}
}
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https://doi.org/10.1128/mBio.02475-19
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