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A genus definition for Bacteria and Archaea based on genome relatedness and taxonomic affiliation

R.A. Barco, G.M. Garrity, J.J. Scott, J.P. Amend, K.H. Nealson, D. Emerson
doi: https://doi.org/10.1101/392480
R.A. Barco
1Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA.
5Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
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G.M. Garrity
3Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA.
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J.J. Scott
4Smithsonian Tropical Research Institute, Panama, Republic of Panama.
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J.P. Amend
1Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA.
2Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
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K.H. Nealson
1Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA.
2Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
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D. Emerson
5Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA.
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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 species and non-type species. More than 750 genomes representing type strains of species from 10 different phyla, and 19 different taxonomic orders/families in Gram-positive/negative, bacterial and archaeal lineages were tested. Overall, all 19 analyzed taxa conserved significant genomic differences between members of a genus and type species of other genera in the same taxonomic family. Bacillus, Flavobacterium, Hydrogenovibrio, Lactococcus, Methanosarcina, Thiomicrorhabdus, Thiomicrospira, Shewanella, and Vibrio are discussed in detail. Less than 1% of the type strains analyzed need reclassification, highlighting that the adoption of the 16S rRNA gene as a taxonomic marker has provided consistency to the classification of microorganisms in recent decades. One exception to this is the genus Bacillus with 61% of type strains needing reclassification, including the human pathogens B. cereus and B. anthracis. The results provide a first line of evidence that the combination of genomic indices provides appropriate resolution to effectively demarcate genera within the current taxonomic framework that is 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 genera. Altogether, these results show that a distinct difference between distant relatives and close relatives at the genome level (i.e., genomic coherence) is an emergent property of genera in Bacteria and Archaea.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 16, 2018.
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A genus definition for Bacteria and Archaea based on genome relatedness and taxonomic affiliation
R.A. Barco, G.M. Garrity, J.J. Scott, J.P. Amend, K.H. Nealson, D. Emerson
bioRxiv 392480; doi: https://doi.org/10.1101/392480
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A genus definition for Bacteria and Archaea based on genome relatedness and taxonomic affiliation
R.A. Barco, G.M. Garrity, J.J. Scott, J.P. Amend, K.H. Nealson, D. Emerson
bioRxiv 392480; doi: https://doi.org/10.1101/392480

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