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Organizing the Global Diversity of Microviruses

Kirchberger, Paul C. and Martinez, Zachary A. and Ochman, Howard (2022) Organizing the Global Diversity of Microviruses. mBio, 13 (3). Art. No. 00588-22. ISSN 2150-7511. PMCID PMC9239249. doi:10.1128/mbio.00588-22. https://resolver.caltech.edu/CaltechAUTHORS:20220520-231754000

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[img] Postscript (FIG S1 Genomic locations of accessory genes in representatives of putative microviral families. Selected genomes show the range of diversity in genome organization with regards to accessory genes within each family. For each family, representative ...) - Supplemental Material
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[img] Postscript (FIG S2 Regions of high sequence identity denote recombination between divergent microviruses.) - Supplemental Material
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[img] PDF (FIG S3 Identifying microviruses in metagenomic datasets. Bipartite protein-sharing networks depict groups of genomes as rectangles, connected by groups of shared proteins (triangles) at ≥30% amino acid identity) - Supplemental Material
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[img] MS Excel (TABLE S1 Curated microvirus genomes) - Supplemental Material
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[img] MS Excel (TABLE S2 Protein clusters (>30% AAI) shared between putative families) - Supplemental Material
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[img] MS Excel (TABLE S3 Microvirus genomes from additional datasets) - Supplemental Material
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[img] MS Excel (TABLE S4 Suggested taxonomy of microviruses) - Supplemental Material
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[img] MS Excel (TABLE S5 Metagenomes investigated in this study) - Supplemental Material
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Abstract

Microviruses encompass an astonishing array of small, single-stranded DNA phages that, due to the surge in metagenomic surveys, are now known to be prevalent in most environments. Current taxonomy concedes the considerable diversity within this lineage to a single family (the Microviridae), which has rendered it difficult to adequately and accurately assess the amount of variation that actually exists within this group. We amassed and curated the largest collection of microviral genomes to date and, through a combination of protein-sharing networks and phylogenetic analysis, discovered at least three meaningful taxonomic levels between the current ranks of family and genus. When considering more than 13,000 microviral genomes from recognized lineages and as-yet-unclassified microviruses in metagenomic samples, microviral diversity is better understood by elevating microviruses to the level of an order that consists of three suborders and at least 19 putative families, each with their respective subfamilies. These revisions enable fine-scale assessment of microviral dynamics: for example, in the human gut, there are considerable differences in the abundances of microviral families both between urban and rural populations and in individuals over time. In addition, our analysis of genome contents and gene exchange shows that microviral families carry no recognizable accessory metabolic genes and rarely, if ever, engage in horizontal gene transfer across microviral families or with their bacterial hosts. These insights bring microviral taxonomy in line with current developments in the taxonomy of other phages and increase the understanding of microvirus biology.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1128/mbio.00588-22DOIArticle
https://github.com/martinez-zacharya/MOP-UPRelated Itemcurated database of microviruses, as well as additional microvirus and metagenomic data sets and code used for analysis
http://www.ncbi.nlm.nih.gov/pmc/articles/pmc9239249/PubMed CentralArticle
ORCID:
AuthorORCID
Kirchberger, Paul C.0000-0002-8387-6440
Martinez, Zachary A.0000-0002-7830-3162
Ochman, Howard0000-0003-1688-7059
Additional Information:© 2022 Kirchberger et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Received 1 March 2022; Accepted 15 April 2022; Published 2 May 2022. We thank Kim Hammond for assistance with figures. This study was funded by NIH award R35GM118038 to H.O. P.C.K. planned the study, P.C.K. and Z.A.M. performed analyses, and P.C.K. and H.O. wrote the manuscript. Data availability. The curated database of microviruses, as well as additional microvirus and metagenomic data sets and code used for analysis, are available at https://github.com/martinez-zacharya/MOP-UP. The authors declare no conflict of interest.
Funders:
Funding AgencyGrant Number
NIHR35GM118038
Subject Keywords:Microviridae, single-stranded DNA viruses, taxonomy, metagenomes
Issue or Number:3
PubMed Central ID:PMC9239249
DOI:10.1128/mbio.00588-22
Record Number:CaltechAUTHORS:20220520-231754000
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20220520-231754000
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:114859
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:24 May 2022 17:34
Last Modified:12 Jul 2022 20:22

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