Characterization of biliary and duodenal microbiota in patients with primary and recurrent choledocholithiasis

Fang Liu; Zi-Kai Wang; Ming-Yang Li; Xiu-Li Zhang; Feng-Chun Cai; Xiang-Dong Wang; Xue-Feng Gao; Wen Li

doi:10.1007/s13755-023-00267-2

Characterization of biliary and duodenal microbiota in patients with primary and recurrent choledocholithiasis

Health Inf Sci Syst. 2024 Apr 4;12(1):29. doi: 10.1007/s13755-023-00267-2. eCollection 2024 Dec.

Authors

Fang Liu^#^{1

2}, Zi-Kai Wang^#^{1

2}, Ming-Yang Li^{1

2}, Xiu-Li Zhang^{1

2}, Feng-Chun Cai², Xiang-Dong Wang², Xue-Feng Gao³, Wen Li^{1

2

4}

Affiliations

¹ Medical School of Chinese PLA, Beijing, China.
² Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, The First Medical Center, No. 28 Fuxing Road, Beijing, 100853 China.
³ Integrative Microecology Clinical Center, Shenzhen Key Laboratory of Gastrointestinal Microbiota and Disease, Shenzhen Clinical Research Center for Digestive Disease, Shenzhen Technology Research Center of Gut Microbiota Transplantation, The Clinical Innovation & Research Center, Shenzhen Hospital, Southern Medical University, Shenzhen, 518000 Guangdong China.
⁴ Minimally Invasive Digestive Disease Center, Beijing and Shenzhen United Family Hospital, Beijing, China.

^# Contributed equally.

PMID: 38584761
PMCID: PMC10994894 (available on 2025-12-01)
DOI: 10.1007/s13755-023-00267-2

Abstract

Purpose: To explore the biliary and duodenal microbiota features associated with the formation and recurrence of choledocholithiasis (CDL).

Methods: We prospectively recruited patients with primary (P-CDL, n = 29) and recurrent CDL (R-CDL, n = 27) for endoscopic retrograde cholangiopancreatography (ERCP). Duodenal mucosa (DM), bile and bile duct stones (BDS) samples were collected in P- and R-CDL patients. DM samples were also collected in 8 healthy controls (HC). The microbiota profile analysis was performed with 16S rRNA gene sequencing.

Results: Short-course antibiotic application before ERCP showed no significant effects in alpha and beta diversities of the biliary and duodenal microbiota in CDL. Alpha diversity showed no difference between DM and bile samples in CDL. The duodenal microbial richness and diversity was lower in both P- and R-CDL than HC. The biliary microbiota composition showed a high similarity between P- and R-CDL. Fusobacterium and Enterococcus were higher abundant in DM, bile, and BDS samples of R-CDL than P-CDL, as well as Escherichia and Klebsiella in bile samples of R-CDL. The enriched duodenal and biliary bacteria in CDL were closely associated with cholecystectomy, inflammation and liver dysfunction. The bile-associated microbiota of R-CDL expressed enhanced capacity of D-glucuronide and D-glucuronate degradation, implicating an elevated level of β-glucuronidase probably produced by enriched Escherichia and Klebsiella in bile.

Conclusions: The duodenal microbiota was in an imbalance in CDL. The duodenal microbiota was probably the main source of the biliary microbiota and was closely related to CDL formation and recurrence. Enterococcus, Fusobacterium, Escherichia and Klebsiella might contribute to CDL recurrence.

Clinical trials: The study was registered at the Chinese Clinical Trial Registry (https://www.chictr.org.cn/index.html, ChiCTR2000033940).

Supplementary information: The online version contains supplementary material available at 10.1007/s13755-023-00267-2.

Keywords: 16S rRNA gene sequencing; Biliary microbiota; Choledocholithiasis; Duodenal microbiota; ERCP.

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