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Metagenomic Sequencing of the Gallbladder Microbiome: Bacterial Diversity Does Not Vary by Surgical Pathology

  • Original Article
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Journal of Gastrointestinal Surgery

Abstract

Introduction

Alterations in the microbiome contribute to the pathogenesis of many gastrointestinal diseases. However, the composition of the microbiome in gallbladder disease is not well described.

Methods

We aimed to characterize the biliary microbiome in cholecystectomy patients. Bile and biliary stones were collected at cholecystectomy for a variety of surgical indications between 2017 and 2019. DNA was extracted and metagenomic sequencing was performed with subsequent taxonomic classification using Kraken2. The fraction of bacterial to total DNA reads, relative abundance of bacterial species, and overall species diversity were compared between pathologies and demographics.

Results

A total of 74 samples were obtained from 49 patients: 46 bile and 28 stones, with matched pairs from 25 patients. The mean age was 48 years, 76% were female, 29% were Hispanic, and 29% of patients had acute cholecystitis. The most abundant species were Klebsiella pneumoniae, Staphylococcus aureus, and Streptococcus pasteurianus. The bacterial fraction in bile and stone samples was higher in acute cholecystitis compared to other non-infectious pathologies (p < 0.05). Neither the diversity nor differential prevalence of specific bacterial species varied significantly between infectious and other non-infectious gallbladder pathologies. Multivariate analysis of the non-infectious group revealed that patients over 40 years of age had increased bacterial fractions (p < 0.05).

Conclusions

Metagenomic sequencing permits characterization of the gallbladder microbiome in cholecystectomy patients. Although a higher prevalence of bacteria was seen in acute cholecystitis, species and diversity were similar regardless of surgical indication. Additional study is required to determine how the microbiome can contribute to the development of symptomatic gallbladder disease.

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Authors and Affiliations

  1. Department of Surgery, Weill Cornell Medicine, New York-Presbyterian Hospital, 1300 York Ave, A1027, New York, NY, 10065, USA

    Jessica Limberg, Caitlin E. Egan, Hector A. Mora, Alexia T. Stamatiou, Timothy M. Ullmann, Maureen D. Moore, Dessislava Stefanova, Jessica W. Thiesmeyer, Brendan M. Finnerty, Toni Beninato, Rasa Zarnegar & Thomas J. Fahey III

  2. Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA

    Gregory Putzel

  3. Department of Surgery, Jamaica Hospital Medical Center, Jamaica, New York, NY, USA

    Katherine McKenzie, R. Jonathan Robitsek & Jeffrey Chan

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Correspondence to Caitlin E. Egan.

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This abstract was presented virtually at the Scientific Forum of the American College of Surgeons’ Clinical Congress October 2020.

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Limberg, J., Egan, C.E., Mora, H.A. et al. Metagenomic Sequencing of the Gallbladder Microbiome: Bacterial Diversity Does Not Vary by Surgical Pathology. J Gastrointest Surg 26, 2282–2291 (2022). https://doi.org/10.1007/s11605-022-05418-6

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