Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing

ABSTRACT Few previous studies have assessed stability and “gold-standard” concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stabil...

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Autores principales:	Doratha A. Byrd, Rashmi Sinha, Kristi L. Hoffman, Jun Chen, Xing Hua, Jianxin Shi, Nicholas Chia, Joseph Petrosino, Emily Vogtmann
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	whole-genome shotgun sequencing microbiome fecal sample collection method FOBT cards FIT tubes Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/015011dedf8541c4a6aa6ddbf503992e
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spelling	oai:doaj.org-article:015011dedf8541c4a6aa6ddbf503992e2021-11-15T15:27:53ZComparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing10.1128/mSphere.00827-192379-5042https://doaj.org/article/015011dedf8541c4a6aa6ddbf503992e2020-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00827-19https://doaj.org/toc/2379-5042ABSTRACT Few previous studies have assessed stability and “gold-standard” concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies. IMPORTANCE A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies.Doratha A. ByrdRashmi SinhaKristi L. HoffmanJun ChenXing HuaJianxin ShiNicholas ChiaJoseph PetrosinoEmily VogtmannAmerican Society for Microbiologyarticlewhole-genome shotgun sequencingmicrobiomefecal sample collection methodFOBT cardsFIT tubesMicrobiologyQR1-502ENmSphere, Vol 5, Iss 1 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	whole-genome shotgun sequencing microbiome fecal sample collection method FOBT cards FIT tubes Microbiology QR1-502
spellingShingle	whole-genome shotgun sequencing microbiome fecal sample collection method FOBT cards FIT tubes Microbiology QR1-502 Doratha A. Byrd Rashmi Sinha Kristi L. Hoffman Jun Chen Xing Hua Jianxin Shi Nicholas Chia Joseph Petrosino Emily Vogtmann Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing
description	ABSTRACT Few previous studies have assessed stability and “gold-standard” concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies. IMPORTANCE A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies.
format	article
author	Doratha A. Byrd Rashmi Sinha Kristi L. Hoffman Jun Chen Xing Hua Jianxin Shi Nicholas Chia Joseph Petrosino Emily Vogtmann
author_facet	Doratha A. Byrd Rashmi Sinha Kristi L. Hoffman Jun Chen Xing Hua Jianxin Shi Nicholas Chia Joseph Petrosino Emily Vogtmann
author_sort	Doratha A. Byrd
title	Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing
title_short	Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing
title_full	Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing
title_fullStr	Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing
title_full_unstemmed	Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing
title_sort	comparison of methods to collect fecal samples for microbiome studies using whole-genome shotgun metagenomic sequencing
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/015011dedf8541c4a6aa6ddbf503992e
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Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing

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