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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
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Gallstone and bile microbiota: A case-control study based on 16S rRNA gene sequencing
Zhong-Xiao Lu1, Yan-Qi Jiang2, Dang-Shou Wang2
1Department of General Surgery, Jinshan Hospital, Fudan University, Shanghai 201508, China.
World Journal of Gastrointestinal Surgery
|September 30, 2025
Summary
Gallstone formation is linked to bile microbiota dysbiosis, specifically an overgrowth of Proteobacteria. Certain bacteria like Lactobacillus may protect against gallstones.
Area of Science:
- Gastroenterology
- Microbiology
- Biliary tract diseases
Background:
- Gallstones (GS) are a common biliary disorder linked to bile stasis, infection, and cholesterol metabolism.
- Emerging research suggests the bile microbiota plays a role in gallstone pathogenesis.
- This case-control study investigated the bile microbiota in gallstone patients.
Purpose of the Study:
- To explore the association between bile microbiota dysbiosis and gallstone formation.
- To analyze the specific composition of bile microbiota in patients with gallstones.
Main Methods:
- Retrospective analysis of 40 patients (25 with GS, 15 GS-free) at Jinshan Hospital (2022-2023).
- Bile samples from 27 patients were analyzed using 16S rRNA gene sequencing.
- Microbial composition and diversity were assessed.
Main Results:
- Gallstone patients exhibited significantly lower microbial diversity (reduced Shannon, Chao, Ace, Sobs; higher Simpson indices).
- Proteobacteria dominated the microbiota in GS patients (91.59%), compared to GS-free patients (79.81%).
- Achromobacter was more abundant in GS patients, while Acinetobacter, Lactobacillus, and Prevotella were enriched in the GS-free group.
Conclusions:
- Bile microbiota dysbiosis, characterized by Proteobacteria overgrowth, may contribute to gallstone formation.
- Lactobacillus enrichment in the bile microbiota might confer a protective effect against gallstones.
- Further studies are warranted to confirm these findings and their clinical implications.

