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dc.contributor.authorBergner, Laura M.
dc.contributor.authorOrton, Richard J.
dc.contributor.authorFilipe, Ana da Silva
dc.contributor.authorShaw, Andrew E.
dc.contributor.authorBecker, Daniel J.
dc.contributor.authorTello, Carlos
dc.contributor.authorBiek, Roman
dc.contributor.authorStreicker, Daniel G.
dc.date.accessioned2019-04-04T19:18:28Z
dc.date.available2019-04-04T19:18:28Z
dc.date.issued2019-01
dc.identifier.citationBergner, Laura M., Richard J. Orton, Ana da Silva Filipe, Andrew E. Shaw, Daniel J. Becker, Carlos Tello, Roman Biek, and Daniel G Streicker. "Using noninvasive metagenomics to characterize viral communities from wildlife." Molecular Ecology Resources 19, no. 1 (January 2019): 128-143. DOI:10.1111/1755-0998.12946.en_US
dc.identifier.issn1755-098X
dc.identifier.urihttps://scholarworks.montana.edu/xmlui/handle/1/15404
dc.description.abstractMicrobial communities play an important role in organismal and ecosystem health. While high‐throughput metabarcoding has revolutionized the study of bacterial communities, generating comparable viral communities has proven elusive, particularly in wildlife samples where the diversity of viruses and limited quantities of viral nucleic acid present distinctive challenges. Metagenomic sequencing is a promising solution for studying viral communities, but the lack of standardized methods currently precludes comparisons across host taxa or localities. Here, we developed an untargeted shotgun metagenomic sequencing protocol to generate comparable viral communities from noninvasively collected faecal and oropharyngeal swabs. Using samples from common vampire bats (Desmodus rotundus), a key species for virus transmission to humans and domestic animals, we tested how different storage media, nucleic acid extraction procedures and enrichment steps affect viral community detection. Based on finding viral contamination in foetal bovine serum, we recommend storing swabs in RNAlater or another nonbiological medium. We recommend extracting nucleic acid directly from swabs rather than from supernatant or pelleted material, which had undetectable levels of viral RNA. Results from a low‐input RNA library preparation protocol suggest that ribosomal RNA depletion and light DNase treatment reduce host and bacterial nucleic acid, and improve virus detection. Finally, applying our approach to twelve pooled samples from seven localities in Peru, we showed that detected viral communities saturated at the attained sequencing depth, allowing unbiased comparisons of viral community composition. Future studies using the methods outlined here will elucidate the determinants of viral communities across host species, environments and time.en_US
dc.description.sponsorshipWellcome Trust and Royal Society (102507/Z/13/Z); Wellcome.Beit Prize (102507/Z/13/A); Medical Research Council (MC_UU_12014/12)en_US
dc.language.isoenen_US
dc.rightsCC BY: This license lets you distribute, remix, tweak, and build upon this work, even commercially, as long as you credit the original creator for this work. This is the most accommodating of licenses offered. Recommended for maximum dissemination and useen_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/legalcodeen_US
dc.titleUsing noninvasive metagenomics to characterize viral communities from wildlifeen_US
dc.typeArticleen_US
mus.citation.extentfirstpage128en_US
mus.citation.extentlastpage143en_US
mus.citation.issue1en_US
mus.citation.journaltitleMolecular Ecology Resourcesen_US
mus.citation.volume19en_US
mus.identifier.categoryLife Sciences & Earth Sciencesen_US
mus.identifier.doi10.1111/1755-0998.12946en_US
mus.relation.collegeCollege of Letters & Scienceen_US
mus.relation.departmentMicrobiology & Immunology.en_US
mus.relation.universityMontana State University - Bozemanen_US
mus.data.thumbpage10en_US


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CC BY: This license lets you distribute, remix, tweak, and build upon this work, even commercially, as long as you credit the original creator for this work. This is the most accommodating of licenses offered. Recommended for maximum dissemination and use
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