Abstract
Abstract
Background
Cholelithiasis is highly prevalent in the Western world and frequently requires surgical or endoscopic intervention. However, the composition and role of the biliary microbiome remain poorly understood. This study aimed to characterize and compare bacterial communities of the biliary niche with saliva and faeces in patients with cholelithiasis.
Methods
In this prospective observational study, patients with symptomatic cholecystolithiasis, chronic or acute cholecystitis, and choledocholithiasis were included. Bacterial community composition was characterized across bile, gallstone, saliva, and faecal samples using 16 S rRNA-based sequencing. Community-level and genus-level differences were assessed according to anatomical niche and clinical diagnosis, complemented by compositional sensitivity analyses and predicted functional profiling.
Results
A total of 227 samples from 81 patients were analyzed. Bacterial community composition was strongly determined by anatomical niche (PERMANOVA, R² = 0.273,
P
-
associated signals in bile, including
Escherichia/Shigella
,
Leptotrichia
,
Serratia
, and
Pseudomonas
. Biliary communities were characterized by taxa including
Enterococcus
,
Escherichia/Shigella
,
Serratia
, and
Pseudomonas
. In bile,
Escherichia/Shigella
increased with inflammatory disease, while
Pseudomonas
decreased; compositionally aware analysis confirmed diagnosis-associated differences for
Escherichia/Shigella
,
Leptotrichia
, and
Serratia
. Predicted bacterial functions showed even stronger anatomical compartmentalization (R² = 0.507,
P
= 0.001), whereas diagnosis-associated functional differences were limited to two MetaCyc pathways in gallstones. Sensitivity analyses provided no evidence that prolonged antibiotic exposure significantly affected biliary bacterial diversity or community composition.
Conclusion
This comprehensive multi-niche analysis demonstrates pronounced taxonomic and predicted functional compartmentalization of bacterial communities across saliva, bile, gallstones, and faeces in patients with cholelithiasis. Diagnosis-associated alterations were predominantly observed within biliary niches, with
Escherichia/Shigella
emerging as a consistent taxon associated with inflammatory biliary disease. These findings identify anatomical niche as a major determinant of bacterial community structure and support disease-associated alterations within the biliary microbiome.
Trial registration
German Clinical Trials Register (Deutsches Register Klinische Studien) DRKS00030566 (retrospectively registered 20250818).