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Article

The Effect of Common Viral Inactivation Techniques on 16S rRNA Amplicon-Based Analysis of the Gut Microbiota

1
Molecular Pathogenesis and Therapeutics Program, University of Missouri, Columbia, MO 65211, USA
2
Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
3
Comparative Medicine Program, University of Missouri, Columbia, MO 65211, USA
4
Metagenomics Center, University of Missouri, Columbia, MO 65211, USA
5
Mutant Mouse Resource and Research Center, University of Missouri, Columbia, MO 65211, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Didier Hober
Microorganisms 2021, 9(8), 1755; https://doi.org/10.3390/microorganisms9081755
Received: 13 July 2021 / Revised: 5 August 2021 / Accepted: 13 August 2021 / Published: 17 August 2021
(This article belongs to the Section Gut Microbiota)
Research investigating the gut microbiome (GM) during a viral infection may necessitate inactivation of the fecal viral load. Here, we assess how common viral inactivation techniques affect 16S rRNA-based analysis of the gut microbiome. Five common viral inactivation methods were applied to cross-matched fecal samples from sixteen female CD-1 mice of the same GM background prior to fecal DNA extraction. The V4 region of the 16S rRNA gene was amplified and sequenced from extracted DNA. Treatment-dependent effects on DNA yield, genus-level taxonomic abundance, and alpha and beta diversity metrics were assessed. A sodium dodecyl sulfate (SDS)-based inactivation method and Holder pasteurization had no effect on measures of microbial richness, while two Buffer AVL-based inactivation methods resulted in a decrease in detected richness. SDS inactivation, Holder pasteurization, and the AVL-based inactivation methods had no effect on measures of alpha diversity within samples or beta diversity between samples. Fecal DNA extracted with TRIzol-treated samples failed to amplify and sequence, making it unsuitable for microbiome analysis. These results provide guidance in the 16S rRNA microbiome analysis of fecal samples requiring viral inactivation. View Full-Text
Keywords: 16S rRNA 1; viral inactivation 2; gut microbiome (GM) 3; fecal DNA extraction 4; SDS 5; TRIzol 6; Buffer AVL 7 16S rRNA 1; viral inactivation 2; gut microbiome (GM) 3; fecal DNA extraction 4; SDS 5; TRIzol 6; Buffer AVL 7
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MDPI and ACS Style

McAdams, Z.; Gustafson, K.; Ericsson, A. The Effect of Common Viral Inactivation Techniques on 16S rRNA Amplicon-Based Analysis of the Gut Microbiota. Microorganisms 2021, 9, 1755. https://doi.org/10.3390/microorganisms9081755

AMA Style

McAdams Z, Gustafson K, Ericsson A. The Effect of Common Viral Inactivation Techniques on 16S rRNA Amplicon-Based Analysis of the Gut Microbiota. Microorganisms. 2021; 9(8):1755. https://doi.org/10.3390/microorganisms9081755

Chicago/Turabian Style

McAdams, Zachary, Kevin Gustafson, and Aaron Ericsson. 2021. "The Effect of Common Viral Inactivation Techniques on 16S rRNA Amplicon-Based Analysis of the Gut Microbiota" Microorganisms 9, no. 8: 1755. https://doi.org/10.3390/microorganisms9081755

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