Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition

ABSTRACT As the number of human microbiome studies expand, it is increasingly important to identify cost-effective, practical preservatives that allow for room temperature sample storage. Here, we reanalyzed 16S rRNA gene amplicon sequencing data from a large sample storage study published in 2016 a...

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Autores principales:	Clarisse Marotz, Kellen J. Cavagnero, Se Jin Song, Daniel McDonald, Stephen Wandro, Greg Humphrey, MacKenzie Bryant, Gail Ackermann, Edgar Diaz, Rob Knight
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2021
Materias:	16S rRNA gene amplicon sequencing benchmarking metagenomics microbiome preservation Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/940dfb6c1f384d6d86218a4b682e1f2e
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spelling	oai:doaj.org-article:940dfb6c1f384d6d86218a4b682e1f2e2021-12-02T17:07:47ZEvaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition10.1128/mSystems.01329-202379-5077https://doaj.org/article/940dfb6c1f384d6d86218a4b682e1f2e2021-04-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.01329-20https://doaj.org/toc/2379-5077ABSTRACT As the number of human microbiome studies expand, it is increasingly important to identify cost-effective, practical preservatives that allow for room temperature sample storage. Here, we reanalyzed 16S rRNA gene amplicon sequencing data from a large sample storage study published in 2016 and performed shotgun metagenomic sequencing on remnant DNA from this experiment. Both results support the initial findings that 95% ethanol, a nontoxic, cost-effective preservative, is effective at preserving samples at room temperature for weeks. We expanded on this analysis by collecting a new set of fecal, saliva, and skin samples to determine the optimal ratio of 95% ethanol to sample. We identified optimal collection protocols for fecal samples (storing a fecal swab in 95% ethanol) and saliva samples (storing unstimulated saliva in 95% ethanol at a ratio of 1:2). Storing skin swabs in 95% ethanol reduced microbial biomass and disrupted community composition, highlighting the difficulties of low biomass sample preservation. The results from this study identify practical solutions for large-scale analyses of fecal and oral microbial communities. IMPORTANCE Expanding our knowledge of microbial communities across diverse environments includes collecting samples in places far from the laboratory. Identifying cost-effective preservatives that will enable room temperature storage of microbial communities for sequencing analysis is crucial to enabling microbiome analyses across diverse populations. Here, we validate findings that 95% ethanol efficiently preserves microbial composition at room temperature for weeks. We also identified the optimal ratio of 95% ethanol to sample for stool and saliva to preserve both microbial load and composition. These results provide rationale for an accessible, nontoxic, cost-effective solution that will enable crowdsourcing microbiome studies, such as The Microsetta Initiative, and lower the barrier for collecting diverse samples.Clarisse MarotzKellen J. CavagneroSe Jin SongDaniel McDonaldStephen WandroGreg HumphreyMacKenzie BryantGail AckermannEdgar DiazRob KnightAmerican Society for Microbiologyarticle16S rRNA gene amplicon sequencingbenchmarkingmetagenomicsmicrobiomepreservationMicrobiologyQR1-502ENmSystems, Vol 6, Iss 2 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	16S rRNA gene amplicon sequencing benchmarking metagenomics microbiome preservation Microbiology QR1-502
spellingShingle	16S rRNA gene amplicon sequencing benchmarking metagenomics microbiome preservation Microbiology QR1-502 Clarisse Marotz Kellen J. Cavagnero Se Jin Song Daniel McDonald Stephen Wandro Greg Humphrey MacKenzie Bryant Gail Ackermann Edgar Diaz Rob Knight Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition
description	ABSTRACT As the number of human microbiome studies expand, it is increasingly important to identify cost-effective, practical preservatives that allow for room temperature sample storage. Here, we reanalyzed 16S rRNA gene amplicon sequencing data from a large sample storage study published in 2016 and performed shotgun metagenomic sequencing on remnant DNA from this experiment. Both results support the initial findings that 95% ethanol, a nontoxic, cost-effective preservative, is effective at preserving samples at room temperature for weeks. We expanded on this analysis by collecting a new set of fecal, saliva, and skin samples to determine the optimal ratio of 95% ethanol to sample. We identified optimal collection protocols for fecal samples (storing a fecal swab in 95% ethanol) and saliva samples (storing unstimulated saliva in 95% ethanol at a ratio of 1:2). Storing skin swabs in 95% ethanol reduced microbial biomass and disrupted community composition, highlighting the difficulties of low biomass sample preservation. The results from this study identify practical solutions for large-scale analyses of fecal and oral microbial communities. IMPORTANCE Expanding our knowledge of microbial communities across diverse environments includes collecting samples in places far from the laboratory. Identifying cost-effective preservatives that will enable room temperature storage of microbial communities for sequencing analysis is crucial to enabling microbiome analyses across diverse populations. Here, we validate findings that 95% ethanol efficiently preserves microbial composition at room temperature for weeks. We also identified the optimal ratio of 95% ethanol to sample for stool and saliva to preserve both microbial load and composition. These results provide rationale for an accessible, nontoxic, cost-effective solution that will enable crowdsourcing microbiome studies, such as The Microsetta Initiative, and lower the barrier for collecting diverse samples.
format	article
author	Clarisse Marotz Kellen J. Cavagnero Se Jin Song Daniel McDonald Stephen Wandro Greg Humphrey MacKenzie Bryant Gail Ackermann Edgar Diaz Rob Knight
author_facet	Clarisse Marotz Kellen J. Cavagnero Se Jin Song Daniel McDonald Stephen Wandro Greg Humphrey MacKenzie Bryant Gail Ackermann Edgar Diaz Rob Knight
author_sort	Clarisse Marotz
title	Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition
title_short	Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition
title_full	Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition
title_fullStr	Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition
title_full_unstemmed	Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition
title_sort	evaluation of the effect of storage methods on fecal, saliva, and skin microbiome composition
publisher	American Society for Microbiology
publishDate	2021
url	https://doaj.org/article/940dfb6c1f384d6d86218a4b682e1f2e
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Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition

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