Using noninvasive metagenomics to characterize viral communities from wildlife

Bergner, L. M. , Orton, R. J. , da Silva Filipe, A. , Shaw, A. E., Becker, D. J., Tello, C., Biek, R. and Streicker, D. G. (2019) Using noninvasive metagenomics to characterize viral communities from wildlife. Molecular Ecology Resources, 19(1), pp. 128-143. (doi: 10.1111/1755-0998.12946) (PMID:30240114) (PMCID:PMC6378809)

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Microbial 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.

Item Type:Articles
Additional Information:Additional funding was provided from the Medical Research Council (MC_UU_12014/12).
Glasgow Author(s) Enlighten ID:Orton, Dr Richard and Da Silva Filipe, Dr Ana and Biek, Professor Roman and Shaw, Dr Andrew and Streicker, Professor Daniel and Bergner, Dr Laura
Authors: Bergner, L. M., Orton, R. J., da Silva Filipe, A., Shaw, A. E., Becker, D. J., Tello, C., Biek, R., and Streicker, D. G.
College/School:College of Medical Veterinary and Life Sciences > School of Infection & Immunity
College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research
College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
Journal Name:Molecular Ecology Resources
ISSN (Online):1755-0998
Published Online:21 September 2018
Copyright Holders:Copyright © 2018 The Authors
First Published:First published in Molecular Ecology Resources 19:128-143
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
634192Managing viral emergence at the interface of bats and livestockDaniel StreickerWellcome Trust (WELLCOTR)102507/Z/13/ZRI BIODIVERSITY ANIMAL HEALTH & COMPMED