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

Abstract

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 storagemore » 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.« less

Authors:
 [1];  [2];  [2];  [2];  [3]; ORCiD logo [2];  [4]; ORCiD logo [4];  [4];  [4];  [2];  [5]
  1. Wannan Medical College, Wuhu (China)
  2. Nanjing Medical Univ. (China)
  3. Key Lab. of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou (China)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. Univ. of Michigan, Ann Arbor, MI (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Key R&D Program of China; National Natural Science Foundation of China (NNSFC); Jiangsu Province; Nanjing Medical University
OSTI Identifier:
1599846
Grant/Contract Number:  
[AC02-05CH11231; 2016YFC1000207; 81630085; gxfxZD2016158; JY-052; KY116NJMUKL16004]
Resource Type:
Accepted Manuscript
Journal Name:
mSphere
Additional Journal Information:
[ Journal Volume: 5; Journal Issue: 1]; Journal ID: ISSN 2379-5042
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; feces; metabolome; microbiome; sampling regions; storage methods

Citation Formats

Liang, Yali, Dong, Tianyu, Chen, Minjian, He, Lianping, Wang, Tingzhang, Liu, Xingyin, Chang, Hang, Mao, Jian-Hua, Hang, Bo, Snijders, Antoine M., Xia, Yankai, and Rao, Krishna. Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles. United States: N. p., 2020. Web. doi:10.1128/mSphere.00763-19.
Liang, Yali, Dong, Tianyu, Chen, Minjian, He, Lianping, Wang, Tingzhang, Liu, Xingyin, Chang, Hang, Mao, Jian-Hua, Hang, Bo, Snijders, Antoine M., Xia, Yankai, & Rao, Krishna. Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles. United States. doi:10.1128/mSphere.00763-19.
Liang, Yali, Dong, Tianyu, Chen, Minjian, He, Lianping, Wang, Tingzhang, Liu, Xingyin, Chang, Hang, Mao, Jian-Hua, Hang, Bo, Snijders, Antoine M., Xia, Yankai, and Rao, Krishna. Wed . "Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles". United States. doi:10.1128/mSphere.00763-19. https://www.osti.gov/servlets/purl/1599846.
@article{osti_1599846,
title = {Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles},
author = {Liang, Yali and Dong, Tianyu and Chen, Minjian and He, Lianping and Wang, Tingzhang and Liu, Xingyin and Chang, Hang and Mao, Jian-Hua and Hang, Bo and Snijders, Antoine M. and Xia, Yankai and Rao, Krishna},
abstractNote = {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.},
doi = {10.1128/mSphere.00763-19},
journal = {mSphere},
number = [1],
volume = [5],
place = {United States},
year = {2020},
month = {1}
}

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