2025-10-14 理化学研究所
腸内細菌の多様性や機能を形成する潜在的な遺伝的メカニズム
<関連情報>
- https://www.riken.jp/press/2025/20251014_1/index.html
- https://www.frontiersin.org/journals/microbiomes/articles/10.3389/frmbi.2025.1635907/full
日本人集団における宿主遺伝子と腸内微生物叢構成の相互作用
Interplay between host genetics and gut microbiome composition in the Japanese population
David Ortega-Reyes,Tadashi Takeuchi,Yusuke Ogata,Takuro Iwami,Wataru Suda,Tetsuya Kubota,Naoto Kubota,Takashi Kadowaki,Kohei Tomizuka,Hiroshi Ohno,Momoko Horikoshi,Chikashi Terao
Frontiers in Microbiomes Published:14 October 2025
DOI:https://doi.org/10.3389/frmbi.2025.1635907
Background: Host genetics significantly influence the composition of the gut microbiota, but this relationship remains poorly understood, especially in non-European populations. This study aims to investigate the associations between host genetic variation and gut microbiome composition in the Japanese population and to assess methodological factors affecting reproducibility in microbiome research.
Methods: We performed whole-genome sequencing on 306 Japanese individuals and obtained their gut microbiome profiles using shotgun metagenomic sequencing. Genome-wide association studies (GWAS) were conducted to identify associations between host genetic variants and the relative abundance of microbial taxa and bacterial pathways. Phenome-wide association studies (PheWAS) were performed on predicted high-impact variants. Additionally, we compared methodological approaches to assess their impact on microbiome composition and reproducibility.
Results: We identified significant associations between host genetic variants and the relative abundance of one bacterial family, one genus, one species and eight bacterial pathways (p ≤ 5×10-8). However, none of these associations surpassed the stringent significance threshold of p ≤ 2.75×10-11. Notably, we were unable to replicate associations reported in prior studies, including those conducted in Japanese populations, even regarding the direction of effects. Our PheWAS analysis uncovered a frameshift variant in the OR6C1 gene (rs5798345-CA) that was significantly associated with an increased abundance of Bacteroides uniformis. Furthermore, comparative analyses highlighted that methodological differences, particularly in sample processing and DNA extraction protocols, substantially influence the observed gut microbiome composition. This variability may be a key factor contributing to the lack of reproducibility across studies.
Conclusion: Our findings enhance the understanding of how host genetics shape the gut microbiota in the Japanese population and underscore the importance of methodological standardization in microbiome research. The identified associations between host genetic variants and specific microbial taxa provide insights into the complex interplay between genetics and the gut microbiome. Addressing methodological discrepancies is crucial for improving reproducibility and advancing knowledge of host–microbiome interactions.
