Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles

ABSTRACT The contribution of human gastrointestinal (GI) microbiota and metabolites to host health has recently become much clearer. However, many confounding factors can influence the accuracy of gut microbiome and metabolome studies, resulting in inconsistencies in published results. In this study...

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Autores principales:	Yali Liang, Tianyu Dong, Minjian Chen, Lianping He, Tingzhang Wang, Xingyin Liu, Hang Chang, Jian-Hua Mao, Bo Hang, Antoine M. Snijders, Yankai Xia
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	feces metabolome microbiome sampling regions storage methods Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/e05cf91dd20849a68cca25125336b216
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spelling	oai:doaj.org-article:e05cf91dd20849a68cca25125336b2162021-11-15T15:27:53ZSystematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles10.1128/mSphere.00763-192379-5042https://doaj.org/article/e05cf91dd20849a68cca25125336b2162020-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00763-19https://doaj.org/toc/2379-5042ABSTRACT The contribution of human gastrointestinal (GI) microbiota and metabolites to host health has recently become much clearer. However, many confounding factors can influence the accuracy of gut microbiome and metabolome studies, resulting in inconsistencies in published results. In this study, we systematically investigated the effects of fecal sampling regions and storage and retrieval conditions on gut microbiome and metabolite profiles from three healthy children. Our analysis indicated that compared to homogenized and snap-frozen samples (standard control [SC]), different sampling regions did not affect microbial community alpha diversity, while a total of 22 of 176 identified metabolites varied significantly across different sampling regions. In contrast, storage conditions significantly influenced the microbiome and metabolome. Short-term room temperature storage had a minimal effect on the microbiome and metabolome profiles. Sample storage in RNALater showed a significant level of variation in both microbiome and metabolome profiles, independent of the storage or retrieval conditions. The effect of RNALater on the metabolome was stronger than the effect on the microbiome, and individual variability between study participants outweighed the effect of RNALater on the microbiome. We conclude that homogenizing stool samples was critical for metabolomic analysis but not necessary for microbiome analysis. Short-term room temperature storage had a minimal effect on the microbiome and metabolome profiles and is recommended for short-term fecal sample storage. In addition, our study indicates that the use of RNALater as a storage medium of stool samples for microbial and metabolomic analyses is not recommended. IMPORTANCE The gastrointestinal microbiome and metabolome can provide a new angle to understand the development of health and disease. Stool samples are most frequently used for large-scale cohort studies. Standardized procedures for stool sample handling and storage can be a determining factor for performing microbiome or metabolome studies. In this study, we focused on the effects of stool sampling regions and stool sample storage conditions on variations in the gut microbiome composition and metabolome profile.Yali LiangTianyu DongMinjian ChenLianping HeTingzhang WangXingyin LiuHang ChangJian-Hua MaoBo HangAntoine M. SnijdersYankai XiaAmerican Society for Microbiologyarticlefecesmetabolomemicrobiomesampling regionsstorage methodsMicrobiologyQR1-502ENmSphere, Vol 5, Iss 1 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	feces metabolome microbiome sampling regions storage methods Microbiology QR1-502
spellingShingle	feces metabolome microbiome sampling regions storage methods Microbiology QR1-502 Yali Liang Tianyu Dong Minjian Chen Lianping He Tingzhang Wang Xingyin Liu Hang Chang Jian-Hua Mao Bo Hang Antoine M. Snijders Yankai Xia Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles
description	ABSTRACT The contribution of human gastrointestinal (GI) microbiota and metabolites to host health has recently become much clearer. However, many confounding factors can influence the accuracy of gut microbiome and metabolome studies, resulting in inconsistencies in published results. In this study, we systematically investigated the effects of fecal sampling regions and storage and retrieval conditions on gut microbiome and metabolite profiles from three healthy children. Our analysis indicated that compared to homogenized and snap-frozen samples (standard control [SC]), different sampling regions did not affect microbial community alpha diversity, while a total of 22 of 176 identified metabolites varied significantly across different sampling regions. In contrast, storage conditions significantly influenced the microbiome and metabolome. Short-term room temperature storage had a minimal effect on the microbiome and metabolome profiles. Sample storage in RNALater showed a significant level of variation in both microbiome and metabolome profiles, independent of the storage or retrieval conditions. The effect of RNALater on the metabolome was stronger than the effect on the microbiome, and individual variability between study participants outweighed the effect of RNALater on the microbiome. We conclude that homogenizing stool samples was critical for metabolomic analysis but not necessary for microbiome analysis. Short-term room temperature storage had a minimal effect on the microbiome and metabolome profiles and is recommended for short-term fecal sample storage. In addition, our study indicates that the use of RNALater as a storage medium of stool samples for microbial and metabolomic analyses is not recommended. IMPORTANCE The gastrointestinal microbiome and metabolome can provide a new angle to understand the development of health and disease. Stool samples are most frequently used for large-scale cohort studies. Standardized procedures for stool sample handling and storage can be a determining factor for performing microbiome or metabolome studies. In this study, we focused on the effects of stool sampling regions and stool sample storage conditions on variations in the gut microbiome composition and metabolome profile.
format	article
author	Yali Liang Tianyu Dong Minjian Chen Lianping He Tingzhang Wang Xingyin Liu Hang Chang Jian-Hua Mao Bo Hang Antoine M. Snijders Yankai Xia
author_facet	Yali Liang Tianyu Dong Minjian Chen Lianping He Tingzhang Wang Xingyin Liu Hang Chang Jian-Hua Mao Bo Hang Antoine M. Snijders Yankai Xia
author_sort	Yali Liang
title	Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles
title_short	Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles
title_full	Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles
title_fullStr	Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles
title_full_unstemmed	Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles
title_sort	systematic analysis of impact of sampling regions and storage methods on fecal gut microbiome and metabolome profiles
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/e05cf91dd20849a68cca25125336b216
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Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles

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