Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles

ABSTRACT Studies of the intestinal microbiome commonly utilize stool samples to measure the microbial composition in the distal gut. However, collection of stool can be difficult from some subjects under certain experimental conditions. Sampling of fecal material using sterile swabs can streamline s...

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Autores principales:	Nicholas A. Bokulich, Juan Maldonado, Dae-Wook Kang, Rosa Krajmalnik-Brown, J. Gregory Caporaso
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	16S rRNA genes gut microbiome sample collection Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/ee9f0bebea5d4e0a824e012fa0f4a40c
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spelling	oai:doaj.org-article:ee9f0bebea5d4e0a824e012fa0f4a40c2021-11-15T15:22:22ZRapidly Processed Stool Swabs Approximate Stool Microbiota Profiles10.1128/mSphere.00208-192379-5042https://doaj.org/article/ee9f0bebea5d4e0a824e012fa0f4a40c2019-04-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00208-19https://doaj.org/toc/2379-5042ABSTRACT Studies of the intestinal microbiome commonly utilize stool samples to measure the microbial composition in the distal gut. However, collection of stool can be difficult from some subjects under certain experimental conditions. Sampling of fecal material using sterile swabs can streamline sample collection, handling, and processing. In this study, we validate the use of swabs of fecal matter to approximate measurements of microbiota in stool using 16S rRNA gene Illumina amplicon sequencing and evaluate the effects of shipping time at ambient temperatures on accuracy. The results indicate that swab samples reliably replicate the stool microbiota bacterial composition, alpha diversity, and beta diversity when swabs are processed quickly (≤2 days) but that sample quality quickly degrades after this period and is accompanied by increased abundances of Enterobacteriaceae. Fresh swabs appear to be a viable alternative to stool sampling when standard collection methods are challenging, but extended exposure to ambient temperatures prior to processing threatens sample integrity. IMPORTANCE Collection of fecal swab samples simplifies handling, processing, and archiving compared to collection of stool. This study confirms that fecal swabs reliably replicate the bacterial composition and diversity of stool samples, provided that the swabs are processed shortly after collection. These findings support the use of fecal swabs, when shipping and handling are done properly, to streamline measurements of intestinal microbiota.Nicholas A. BokulichJuan MaldonadoDae-Wook KangRosa Krajmalnik-BrownJ. Gregory CaporasoAmerican Society for Microbiologyarticle16S rRNA genesgut microbiomesample collectionMicrobiologyQR1-502ENmSphere, Vol 4, Iss 2 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	16S rRNA genes gut microbiome sample collection Microbiology QR1-502
spellingShingle	16S rRNA genes gut microbiome sample collection Microbiology QR1-502 Nicholas A. Bokulich Juan Maldonado Dae-Wook Kang Rosa Krajmalnik-Brown J. Gregory Caporaso Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles
description	ABSTRACT Studies of the intestinal microbiome commonly utilize stool samples to measure the microbial composition in the distal gut. However, collection of stool can be difficult from some subjects under certain experimental conditions. Sampling of fecal material using sterile swabs can streamline sample collection, handling, and processing. In this study, we validate the use of swabs of fecal matter to approximate measurements of microbiota in stool using 16S rRNA gene Illumina amplicon sequencing and evaluate the effects of shipping time at ambient temperatures on accuracy. The results indicate that swab samples reliably replicate the stool microbiota bacterial composition, alpha diversity, and beta diversity when swabs are processed quickly (≤2 days) but that sample quality quickly degrades after this period and is accompanied by increased abundances of Enterobacteriaceae. Fresh swabs appear to be a viable alternative to stool sampling when standard collection methods are challenging, but extended exposure to ambient temperatures prior to processing threatens sample integrity. IMPORTANCE Collection of fecal swab samples simplifies handling, processing, and archiving compared to collection of stool. This study confirms that fecal swabs reliably replicate the bacterial composition and diversity of stool samples, provided that the swabs are processed shortly after collection. These findings support the use of fecal swabs, when shipping and handling are done properly, to streamline measurements of intestinal microbiota.
format	article
author	Nicholas A. Bokulich Juan Maldonado Dae-Wook Kang Rosa Krajmalnik-Brown J. Gregory Caporaso
author_facet	Nicholas A. Bokulich Juan Maldonado Dae-Wook Kang Rosa Krajmalnik-Brown J. Gregory Caporaso
author_sort	Nicholas A. Bokulich
title	Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles
title_short	Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles
title_full	Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles
title_fullStr	Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles
title_full_unstemmed	Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles
title_sort	rapidly processed stool swabs approximate stool microbiota profiles
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/ee9f0bebea5d4e0a824e012fa0f4a40c
work_keys_str_mv	AT nicholasabokulich rapidlyprocessedstoolswabsapproximatestoolmicrobiotaprofiles AT juanmaldonado rapidlyprocessedstoolswabsapproximatestoolmicrobiotaprofiles AT daewookkang rapidlyprocessedstoolswabsapproximatestoolmicrobiotaprofiles AT rosakrajmalnikbrown rapidlyprocessedstoolswabsapproximatestoolmicrobiotaprofiles AT jgregorycaporaso rapidlyprocessedstoolswabsapproximatestoolmicrobiotaprofiles
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Rapidly Processed Stool Swabs Approximate Stool Microbiota Profiles

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