Biliary Microbiota in Choledocholithiasis and Correlation With Duodenal Microbiota

Study information

Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-18

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

33996618

DOI Digital object identifier for electronic documents.

https://doi.org/10.3389/fcimb.2021.625589

URI

Authors

Han J, Wu S, Fan Y, Tian Y, Kong J

Journal

Frontiers in cellular and infection microbiology

Year

2021

Keywords:

antimicrobial resistance, biliary microbiota, choledocholithiasis, duodenal microbiota, duodenal–biliary reflux

BACKGROUND: The pathogenesis of choledocholithiasis is closely related to the role of bacteria. However, little is known about the predictive role of bile bacteria in clinical conditions of patients and the compositional and functional characteristics of biliary microbiota in choledocholithiasis. METHODS: To investigate the predictive value of biliary bacteria, clinical data of 488 patients with choledocholithiasis were collected. The predictive value of common bile bacteria to patients' clinical conditions was analyzed by logistic regression. Samples of bile and corresponding duodenal juice from 10 selected patients with choledocholithiasis were obtained, and the composition and function of microbial communities were analyzed based on 16S rRNA sequencing and Tax4Fun. RESULTS: The clinical conditions of patients with choledocholithiasis, such as recurrence, the severity of acute cholangitis, and duration of hospital stay were closely related to different species of bile bacteria as well as antimicrobial-resistant bacteria. Employing 16S rRNA sequencing, the dominant phyla of biliary and duodenal microbiota were Proteobacteria and Firmicutes. The top three core microbiota at the genus level were Escherichia-Shigella, Fusobacterium, and Enterococcus. Escherichia coli accounted for the most abundant annotated species in both. Differences in composition between biliary and duodenal microbiota were not significant according to the alpha and beta diversities. Differential abundant features were not found in biliary microbiota indicated by A linear discriminant analysis effective size algorithm. The major pathways identified in biliary and duodenal microbiota were related to membrane transport, translation, replication and repair, carbohydrate and amino acid metabolism. However, no significant difference in those major pathways, as well as antimicrobial-resistance patterns, was observed between biliary and duodenal microbiota. CONCLUSION: Our study first demonstrates the predictive contribution of biliary bacteria to the clinical conditions of patients with choledocholithiasis, and then it offers new insights into the compositional and functional features of biliary and duodenal microbiota. Similarities between biliary and duodenal microbiota support the theory of bacterial duodenal-biliary reflux in patients with choledocholithiasis. Meanwhile, when it is impracticable to obtain a bile sample, duodenal juice may be used as an alternative for bacterial culture and susceptibility tests.

Experiment 1

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-18

Curated date: 2023/12/14

Curator: Folakunmi

Revision editor(s): Folakunmi

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Duodenum , Bile duct Proximal intestine,Upper intestine,Duodenum,duodenum,Bile tube,Biliary duct,Gall duct,Hepatic duct,Bile duct,bile duct

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Sampling site Sampling site,sampling site

Group 0 name Corresponds to the control (unexposed) group for case-control studies: biliary microbiota

Group 1 name Corresponds to the case (exposed) group for case-control studies: duodenal microbiota

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: duodenal juice samples from patients with choledocholithiasis

Group 0 sample size Number of subjects in the control (unexposed) group: 10

Group 1 sample size Number of subjects in the case (exposed) group: 10

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 4 weeks

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 4

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: unchanged

Richness Number of species: unchanged

Signature 1

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Reviewed Marked as Reviewed by ChiomaBlessing on 2023-12-18

Curated date: 2023/12/14

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: figure 2D

Description: microbial taxa characterizing duodenal juice from bile in patients with choledocholithiasis as determined by LEfSe

Abundance in Group 1: increased abundance in duodenal microbiota

NCBI	Quality Control	Links
Actinomycetota
Bacilli
Lactobacillales
Streptococcaceae
Streptococcus
unclassified Actinomycetota

Revision editor(s): Folakunmi