Biogeographic Study of Human Gut-Associated CrAssphage Suggests Impacts From Industrialization and Recent Expansion

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dc.contributor.authorHonap, Tanvi P.
dc.contributor.authorSankaranarayanan, Krithivasan
dc.contributor.authorSchnorr, Stephanie L.
dc.contributor.authorOzga, Andrew T.
dc.contributor.authorWarinner, Christina
dc.contributor.authorLewis Jr., Cecil M.
dc.date.accessioned2020-04-16T17:00:45Z
dc.date.available2020-04-16T17:00:45Z
dc.date.issued2020-01-15
dc.description.abstractCrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are associated with specific human populations. In this study, we screened publicly available human gut metagenomic data from 3,341 samples for the presence of crAssphage sensu stricto (NC_024711.1). We found that crAssphage prevalence is low in traditional, hunter-gatherer populations, such as the Hadza from Tanzania and Matses from Peru, as compared to industrialized, urban populations. Statistical comparisons showed no association of crAssphage prevalence with variables such as age, sex, body mass index, and health status of individuals. Phylogenetic analyses show that crAssphage strains reconstructed from the same individual over multiple time-points, cluster together. CrAssphage strains from individuals from the same study population do not always cluster together. Some evidence of clustering is seen at the level of broadly defined geographic regions, however, the relative positions of these clusters within the crAssphage phylogeny are not well-supported. We hypothesize that this lack of strong biogeographic structuring is suggestive of an expansion event within crAssphage. Using a Bayesian dating approach, we estimate that this expansion has occurred fairly recently. Overall, we determine that crAssphage presence is associated with an industrialized lifestyle and the absence of strong biogeographic structuring within global crAssphage strains is likely due to a recent population expansion within this bacteriophage.en_US
dc.description.peerreviewYesen_US
dc.description.sponsorshipThis study was supported by a grant from the National Institutes of Health (https://www.nih.gov/), NIH R01 GM089886, awarded to C.M.L., C.W., and K.S. Open Access fees paid for in whole or in part by the University of Oklahoma Libraries.en_US
dc.identifier.citationHonap TP, Sankaranarayanan K, Schnorr SL, Ozga AT, Warinner C, Lewis CM Jr. (2020). Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion. PLoS ONE 15(1): e0226930. https://doi.org/10.1371/journal.pone.0226930en_US
dc.identifier.doi10.1371/journal.pone.0226930en_US
dc.identifier.urihttps://hdl.handle.net/11244/323884
dc.languageen_USen_US
dc.rightsAttribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectbacteriophagesen_US
dc.subjectcrAssphageen_US
dc.subjectphylogenetic analysisen_US
dc.subjectBiogeographyen_US
dc.subjectphylogeographyen_US
dc.subjectmetagenomicsen_US
dc.subjectbacteroidesen_US
dc.titleBiogeographic Study of Human Gut-Associated CrAssphage Suggests Impacts From Industrialization and Recent Expansionen_US
dc.typeArticleen_US
ou.groupCollege of Arts and Sciences::Department of Anthropologyen_US

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