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Proposal of a health gut microbiome index based on a meta-analysis of Korean and global population datasets

  • Systems and Synthetic Microbiology and Bioinformatics
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Abstract

The disruption of the human gut microbiota has been linked to host health conditions, including various diseases. However, no reliable index for measuring and predicting a healthy microbiome is currently available. Here, the sequencing data of 1,663 Koreans were obtained from three independent studies. Furthermore, we pooled 3,490 samples from public databases and analyzed a total of 5,153 fecal samples. First, we analyzed Korean gut microbiome covariates to determine the influence of lifestyle on variation in the gut microbiota. Next, patterns of microbiota variations across geographical locations and disease statuses were confirmed using a global cohort and di-sease data. Based on comprehensive comparative analysis, we were able to define three enterotypes among Korean cohorts, namely, Prevotella type, Bacteroides type, and outlier type. By a thorough categorization of dysbiosis and the evaluation of microbial characteristics using multiple datasets, we identified a wide spectrum of accuracy levels in classifying health and disease states. Using the observed microbiome patterns, we devised an index named the gut microbiome index (GMI) that could consistently predict health conditions from human gut microbiome data. Compared to ecological metrics, the microbial marker index, and machine learning approaches, GMI distinguished between healthy and non-healthy individuals with a higher accuracy across various datasets. Thus, this study proposes a potential index to measure health status of gut microbiome that is verified from multiethnic data of various diseases, and we expect this model to facilitate further clinical application of gut microbiota data in future.

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The datasets generated and analyzed during the current study are available from the corresponding author upon reasonable request.

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Acknowledgements

This research was funded by ChunLab, Inc., and received no external funding.

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Authors and Affiliations

  1. ChunLab Inc., Seoul, 06194, Republic of Korea

    Hyun-Seok Oh, Uigi Min, Hye** Jang, Namil Kim, Jeongmin Lim, Mauricio Chalita & Jongsik Chun

  2. Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea

    Hyun-Seok Oh & Jongsik Chun

  3. School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea

    Jongsik Chun

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Conflict of Interest All other authors are employees of ChunLab, Inc.

Ethical Statements The study was conducted according to the guidelines of the Declaration of Helsinki and the research protocol was approved by Institutional Review Boards (IRB). The studies were approved by the Public Institutional Bioethics Committee designated by the MOHW (IRB:P01-201804-31-004, P01-201905-11-004), the Institutional Review Board of Samsung Medical Center (IRB:2016-06-040), and the Institutional Review Board of Myong Ji Hospital (IRB:2018-08-020).

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Oh, HS., Min, U., Jang, H. et al. Proposal of a health gut microbiome index based on a meta-analysis of Korean and global population datasets. J Microbiol. 60, 533–549 (2022). https://doi.org/10.1007/s12275-022-1526-0

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