Variation in the metagenomic analysis of fecal microbiome composition calls for a standardized operating approach

The reproducibility of human gut microbiome studies has been suboptimal across cohorts and study design choices. One possible reason for the disagreement is the introduction of systemic biases due to differences in methodologies. In our study, we utilized microbial metagenomic data sets from 2,722 f...

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Published inMicrobiology spectrum Vol. 12; no. 12; p. e0151624
Main Authors Xu, Zhilu, Yeoh, Yun Kit, Tun, Hein M., Fei, Na, Zhang, Jingwan, Morrison, Mark, Kamm, Michael A., Yu, Jun, Chan, Francis Ka Leung, Ng, Siew C.
Format Journal Article
LanguageEnglish
Published United States American Society for Microbiology 30.10.2024
Subjects
batch effect
DNA extraction
Human Microbiome
metagenomics
microbiome
Research Article
batch effect
DNA extraction
microbiome
metagenomics
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Summary:The reproducibility of human gut microbiome studies has been suboptimal across cohorts and study design choices. One possible reason for the disagreement is the introduction of systemic biases due to differences in methodologies. In our study, we utilized microbial metagenomic data sets from 2,722 fecal samples generated from a single research center to examine the extent to which sample storage and DNA extraction influence the quantification of microbial composition and compared this variable with other sources of technical and biological variation. Our research highlights the impact of DNA extraction methods when analyzing microbiome data and suggests that the microbiome profile may be influenced by differences in the extraction efficiency of bacterial species. With metagenomics sequencing being increasingly used in clinical biology, our findings provide insight into the challenges using metagenomics sequencing in clinical diagnostics, where the detection of certain species and its abundance relative to a “healthy reference” is key.
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F.K.L.C. is a Board Member of CUHK Medical Centre. He is a co-founder, non-executive Board Chairman, and shareholder of GenieBiome Ltd. He receives patent royalties through his affiliated institutions. He has received fees as an advisor and honoraria as a speaker for Eisai Co. Ltd., AstraZeneca, Pfizer Inc., Takeda Pharmaceutical Co., and Takeda (China) Holdings Co. Ltd. S.C.N. has served as an advisory board member for Pfizer, Ferring, Janssen, and Abbvie and received honoraria as a speaker for Ferring, Tillotts, Menarini, Janssen, Abbvie, and Takeda. S.C.N. has received research grants through her affiliated institutions from Olympus, Ferring, and Abbvie. S.C.N. is a scientific co-founder and shareholder of GenieBiome Ltd. S.C.N. receives patent royalties through her affiliated institutions. Z.X., Y.K.Y., H.M.T., J.Z., F.K.L.C., and S.C.N. are named inventors of patent applications held by the CUHK and MagIC that cover the therapeutic and diagnostic use of microbiome.
ISSN:2165-0497
2165-0497
DOI:10.1128/spectrum.01516-24