Application of Next-Generation Sequencing on Biliary Microbiota in Patients Undergoing ERCP: The “MICROBILE” Registry

Aims The biliary tract, previously considered sterile, is now recognized as a reservoir for diverse microbial communities, particularly in patients with hepatobiliary diseases. This prospective observational study aimed to explore differences the microbial composition of bile in patients affected by benign and malignant biliary obstruction which needed and endoscopic biliary drainage, with the aim of providing insights into the microbiota's role in pancreatobiliary diseases.

Methods Forty-eight patients with naïve papilla undergoing ERCP for biliary obstruction (benign: n=24; malignant: n=24) were prospectively enrolled between July 2022 and August 2023. Bile samples were collected after bile duct cannulation and at the end of the procedure. Next-generation sequencing (NGS) was performed to identify microbial taxa, quantifying their abundances as relative read percentages. Clinical characteristics, bile cultures, and follow-up data were collected and correlated to microbial patterns.

Results The NGS revealed significant differences in the biliary microbiota between the benign and malignant group. In detail, some commensals like Streptococci and Prevotella were detected in both clues, although the presencence of Streptococcus sp. was significantly higher in the benign group samples, compare to the malignant once (75% vs 69%, p=0.00036). Similarly, Prevotella sp. was detected in 42% of benign cases and 38% of malignant cases (p=0.00039), highlighting its widespread presence across both conditions. A specific pattern of microrganisms including Veillonella sp., Porphyromonas sp., Neisseria sp., Haemophilus sp., Gemella sp., and Fusobacterium sp. was predominantly associated with benign diseases. In contrast, Granulicatella sp. and Escherichia sp. showed stronger associations with malignant jaundice.

Conclusions The biliary microbiota demonstrates a substantial variability between benign and malignant conditions for patients with naive papilla that underwent ERCP, with specific microbial patterns associated with each condition. Streptococcus sp. and Prevotella sp. were universally present, while some microrganisms showed an association with benign or malignant jaundice. These findings underscore the importance of microbial profiling in understanding biliary diseases and suggest a potential diagnostic and therapeutic role for microbiota-based strategies. Further research is needed to elucidate these relationships and their clinical implications [1] [2] [3].

 

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Conflicts of Interest

Authors do not have any conflict of interest to disclose.

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• 2 Nicoletti A, Ponziani FR, Nardella E, Ianiro G, Gasbarrini A, Zileri Dal Verme L.. Biliary tract microbiota: a new kid on the block of liver diseases?. Eur Rev Med Pharmacol Sci 2020; 24 (05): 2750-2775 PMID: 32196626
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Publication History

Article published online:
27 March 2025