Using noninvasive metagenomics to characterize viral communities from wildlife.

Molecular Ecology Resources
Laura M BergnerDaniel G Streicker

Abstract

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 undetectab...Continue Reading

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Citations

Mar 16, 2019·Integrative and Comparative Biology·Daniel J BeckerDaniel G Streicker
Sep 29, 2019·Molecular Ecology·Laura M BergnerDaniel G Streicker
Dec 20, 2019·The Journal of Animal Ecology·Daniel J BeckerRaina K Plowright
Dec 12, 2019·Molecular Ecology Resources·Shawn R NarumBenjamin Sibbett
Nov 20, 2019·Nature Ecology & Evolution·Cara E Brook
Aug 21, 2020·Microbiology Resource Announcements·Laura M BergnerDaniel G Streicker
Nov 25, 2020·Nature Communications·Megan E GriffithsDaniel G Streicker
Jan 24, 2021·Zoonoses and Public Health·Laura M BergnerDaniel G Streicker
Feb 8, 2021·Trends in Ecology & Evolution·Jennifer L MalmbergSue VandeWoude
Jan 6, 2021·Proceedings of the National Academy of Sciences of the United States of America·Laura M BergnerDaniel G Streicker
Mar 14, 2021·Molecular Ecology Resources·Patricia GilSerafin Gutierrez
Apr 30, 2021·The Journal of Applied Ecology·Daniel J BeckerMatthew M Chumchal
Sep 21, 2021·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Colin J CarlsonPaul W Webala

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Datasets Mentioned

BETA
PRJNA414273

Methods Mentioned

BETA
PCR
density gradient centrifugation
Illumina sequencing

Software Mentioned

MEGAN Community Edition
R
r package vegan
lme4

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