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

Journal Article · · mSphere
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  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)
+ Show Author Affiliations

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.

Research Organization:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC); National Key Research and Development Program of China; National Natural Science Foundation of China (NSFC); Jiangsu Province; Nanjing Medical University
Grant/Contract Number:
AC02-05CH11231; 2016YFC1000207; 81630085; gxfxZD2016158; JY-052; KY116NJMUKL16004
OSTI ID:
1599846
Journal Information:
mSphere, Vol. 5, Issue 1; ISSN 2379-5042
Publisher:
American Society for MicrobiologyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 23 works
Citation information provided by
Web of Science

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  • Enrique, Zambrana, Luis; Andrea, Monteagudo,; Sylvia, Becker-Dreps,
  • The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/fq68-bw87
text January 2015

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59 BASIC BIOLOGICAL SCIENCES
feces
metabolome
microbiome
sampling regions
storage methods