Gallstone and bile microbiota: A case-control study based on 16S rRNA gene sequencing

doi:10.4240/wjgs.v17.i9.109521

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World Journal of Gastrointestinal Surgery

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1948-9366

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

Case Control Study

World J Gastrointest Surg. Sep 27, 2025; 17(9): 109521
Published online Sep 27, 2025. doi: 10.4240/wjgs.v17.i9.109521

Gallstone and bile microbiota: A case-control study based on 16S rRNA gene sequencing

Zhong-Xiao Lu, Yan-Qi Jiang, Dang-Shou Wang, Yu-Ting Song, Xiao-Ming Jiang, Fu-Jian Xu, Jie Tang, Bing Li, Wen-Hai Huang

Zhong-Xiao Lu, Xiao-Ming Jiang, Fu-Jian Xu, Jie Tang, Wen-Hai Huang, Department of General Surgery, Jinshan Hospital, Fudan University, Shanghai 201508, China

Yan-Qi Jiang, Dang-Shou Wang, Yu-Ting Song, Bing Li, Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, Shanghai 201508, China

Co-first authors: Zhong-Xiao Lu and Yan-Qi Jiang.

Co-corresponding authors: Bing Li and Wen-Hai Huang.

Author contributions: Lu ZX collected data, revised and supplemented the manuscript; Jiang YQ analyzed and interpreted the data and wrote the first draft of the manuscript; Lu ZX and Jiang YQ contributed equally to this article, they are the co-first authors of this manuscript; Wang DS, Song YT, Jiang XM, Xu FJ, and Tang J performed the research; Li B revised the manuscript, directed and organized research; Huang WH participated in the interpretation of the data and made important modifications; Li B and Huang WH edited manuscripts, they contributed equally to this article, they are the co-corresponding authors of this manuscript; and all authors have read and agreed to the published version of the manuscript.

Supported by the Youth Scientific Research Launch Fund Project of Jinshan Hospital, Affiliated with Fudan University, No. JYQN-LC-202214.

Institutional review board statement: This study was approved by the Medical Ethics Committee of Jinshan Hospital, Fudan University, approval No. JIEC 2022-S53.

Informed consent statement: All study participants, or their legal guardian, provided informed written consent prior to study enrollment.

Conflict-of-interest statement: All the authors report no relevant conflicts of interest for this article.

STROBE statement: The authors have read the STROBE Statement-checklist of items, and the manuscript was prepared and revised according to the STROBE Statement-checklist of items.

Data sharing statement: Technical appendix, statistical code, and dataset available from the corresponding author at li_bing@fudan.edu.cn.

Open Access: This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: https://creativecommons.org/Licenses/by-nc/4.0/

Corresponding author: Bing Li, Researcher, Research Center for Clinical Medicine, Jinshan Hospital, Fudan University, No. 1508 Longhang Road, Shanghai 201508, China. li_bing@fudan.edu.cn

Received: May 14, 2025
Revised: June 4, 2025
Accepted: July 18, 2025
Published online: September 27, 2025
Processing time: 133 Days and 20 Hours

Abstract

BACKGROUND

Gallstone (GS), a prevalent biliary disorder, is associated with bile stasis, infection, and cholesterol metabolism. Recent research highlights the potential role of bile microbiota in GS pathogenesis. This is a case control study conducted at Jinshan Hospital between 2022 and 2023.

AIM

To investigate the relationship between bile microbiota dysbiosis and GS formation, and analyze bile microbiota composition in GS patients.

METHODS

This is a retrospective analysis conducted at Jinshan Hospital between 2022 and 2023. A total of 40 patients were analyzed, including 25 with GS and 15 with GS-free (GSF). Bile samples from 27 patients were analyzed using 16S rRNA gene sequencing to assess microbial composition.

RESULTS

Significant differences were found in bile acid profiles between GS and GSF groups, with lower microbial diversity in GS patients, indicated by reduced Shannon, Chao, Ace, and Sobs indices, and a higher Simpson index. At the phylum level, the most abundant taxa in GS patients were Proteobacteria (91.59%), Firmicutes (2.90%), and Actinobacteria (1.70%), while Proteobacteria (79.81%), Firmicutes (9.67%), and Bacteroidota (3.80%) were predominated in the GSF group. Notably, Achromobacter was more abundant in GS patients, while Acinetobacter, Lactobacillus, and Prevotella were enriched in the GSF group, suggesting their potential protective role against GS formation.

CONCLUSION

Dysbiosis, particularly overgrowth of Proteobacteria, may contribute to gallstone formation, while Lactobacillus could play a protective role. Further research is needed to validate these findings.

Keywords: Gallstones; Bile microbiota; 16S rRNA sequencing; Diversity analysis; Genus identification

Core Tip: This retrospective study analyzed bile microbiota composition in 40 patients. Results demonstrated that samples from gallstone patients exhibited significantly reduced overall microbial diversity alongside a striking dominance of Proteobacteria. In contrast, bile samples from gallstone-free individuals showed relative enrichment in health-associated genera, including protective taxa like Lactobacillus. The findings indicate that dysbiosis within the bile microbiome, particularly the overgrowth of Proteobacteria, actively drives gallstone pathogenesis. This suggests that modulating the bile microbiota represents a promising novel therapeutic avenue for gallstone prevention or treatment through targeted interventions.