Comprehensive Evaluation and Application of Experimental Sources of Variation in Gut Microbiome Sequencing Studies

Ke-lin XU; Yue Zhuang; Si-bo Zhu; Jiang-li Xue; Yan-feng Jiang; Zi-yu Yuan; Chen Suo; Tie-jun Zhang; Ming LV; Xing-dong Chen; Si-bo Zhu; Yan-feng Jiang; Jiu-cun Wang; Xing-dong Chen; Si-bo Zhu; Yan-feng Jiang; Xing-dong Chen; Chen Suo; Tie-jun Zhang; Ming LV

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Comprehensive Evaluation and Application of Experimental Sources of Variation in Gut Microbiome Sequencing Studies

Author: Ke-Lin XU ¹ ; Yue ZHUANG ¹ ; Si-Bo ZHU ² ; Jiang-Li XUE ² ; Yan-Feng JIANG ² ; Zi-Yu YUAN ² ; Chen SUO ² ; Tie-Jun ZHANG ² ; Ming LV ² ; Xing-Dong CHEN ² ; Si-Bo ZHU ³ ; Yan-Feng JIANG ³ ; Jiu-Cun WANG ³ ; Xing-Dong CHEN ³ ; Si-Bo ZHU ⁴ ; Yan-Feng JIANG ⁴ ; Xing-Dong CHEN ⁴ ; Chen SUO ⁵ ; Tie-Jun ZHANG ⁵ ; Ming LV ⁶
Author Information

1. Department of Biostatistics, School of Public Health, Fudan University
2. Fudan University Taizhou, Institute of Health Sciences
3. Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University
4. Human Phenome Institute, Fudan University
5. Department of Epidemiology, School of Public Health, Fudan University
6. Clinical Epidemiology Unit, Qilu Hospital of Shandong University
Publication Type:Journal Article
Keywords: 16S amplication sequencing; empirical Bayes; gut microbiome sequencing; taxonomic profiles; whole-metagenome shotgun (WMS)
From: Chinese Journal of Biochemistry and Molecular Biology 2022;38(7):959-970
CountryChina
Language:Chinese
Abstract: Gut microbiome sequencing studies have great potential to translate microbial analysis outcomes into human health research. Sequencing strategies of 16S amplicon and whole-metagenome shotgun (WMS) are two main methods in microbiome research with respective advantages. However, how sample heterogeneity, sequencers and library preparation protocols affect the sequencing reproducibility of gut microbiome needs further investigation. This study aims to provide a reference for the selection of sequencing technologies by comparing differences in microbial composition from different sampling sites. The results of three widely adopted sequencers showed that the technical repetition correlation (r= 0. 94) was high in WMS method, while the biological repetition correlation (r = 0. 69) was low. Bray-Curtis distance identified that dissimilarity from biological replicates was larger than that of technical replicates (P<0. 001). In addition, dissimilarity and specific taxonomic profiles were observed between 16S and WMS datasets. Our results imply that homogenization is a necessary step before sample DNA extraction. The sequencers contributed less to taxonomic variation than the library preparation protocols. We developed an empirical Bayes approach that " borrowed information" in calculations and analyzed batch effect parameters using standardized data and prior distributions of (non-) parameters, which may improve population comparability between 16S and WMS and provide a basis for further application to fusion analysis of published 16S and microbial datasets.