Cited by 234Gut microbiota and healthGallbladder and Bile Duct DisordersMicrobial Community Ecology and Physiology

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Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study

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Wu, Tao, Zhang, Zhigang, Liu, Bin, Hou, Dezhi, Liang, Yun, Zhang, Jie, Shi, Peng·2013·BMC Genomics

DOI 10.1186/1471-2164-14-669PMC PMC3851472

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Abstract

BACKGROUND: Elucidating gut microbiota among gallstone patients as well as the complex bacterial colonization of cholesterol gallstones may help in both the prediction and subsequent lowered risk of cholelithiasis. To this end, we studied the composition of bacterial communities of gut, bile, and gallstones from 29 gallstone patients as well as the gut of 38 normal individuals, examining and analyzing some 299, 217 bacterial 16S rRNA gene sequences from 120 samples. RESULTS: First, as compared with normal individuals, in gallstone patients there were significant (P < 0.001) increases of gut bacterial phylum Proteobacteria and decreases of three gut bacterial genera, Faecalibacterium, Lachnospira, and Roseburia. Second, about 70% of gut bacterial operational taxonomic units (OTUs) from gallstone patients were detectable in the biliary tract and bacteria diversity of biliary tract was significantly (P < 0.001) higher than that of gut. Third, analysis of the biliary tract core microbiome (represented by 106 bacteria OTUs) among gallstone patients showed that 33.96% (36/106) of constituents can be matched to known bacterial species (15 of which have publicly available genomes). A genome-wide search of MDR, BSH, bG, and phL genes purpotedly associated with the formation of cholesterol gallstones showed that all 15 species with known genomes (e.g., Propionibacterium acnes, Bacteroides vulgates, and Pseudomonas putida) contained at least contained one of the four genes. This finding could potentially provide underlying information needed to explain the association between biliary tract microbiota and the formation of cholesterol gallstones. CONCLUSIONS: To the best of our knowledge, this is the first study to discover gut microbiota dysbiosis among gallstone patients, the presence of which may be a key contributor to the complex bacteria community assembly linked with the presence of cholesterol gallstones. Likewise, this study also provides the first large-scale glimpse of biliary tract microbiota potentially associated with cholesterol gallstones. Such a characterization of the biliary tract core microbiome has potentially important biological and medical implications regarding the role of bacteria in the formation cholesterol gallstones.

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Figure 1 Phyla level comparisons of microbial components between the gut and biliary tract. Only top nine phyla shown. ***P < 0.001.CC BY · PubMed Central

Figure 2 Genera level comparisons of microbial components between gut and biliary tract. In total, 38 genera distributions are shown, including those genera of each type of sample with relative abundance of at least 0.01%, respectively. Taxons marked by stars were unclassified. C., Clostridiaceae family. L., Lachnospiraceae family. R., Ruminococcaceae family. *P < 0.05.CC BY · PubMed Central

Figure 3 Microbiota analysis of separates samples based upon where they live in the community. Hierarchical average clustering based on the Spearman/Pearson correlation coefficients of the proportion of all taxons, filtered for taxonomic variables with over 50% percent zeroes. Non-informative variables are characterized using the coefficient of variation (mean/standard deviation). Data normalization between samples was conducted by Sum, and those between taxons Pareto Scaling (mean-centered and divided by the square root of standard deviation of each variable). In total, 35 taxonomic features are shown in the heatmap, with statistical significance among four types of samples based on T-test/ANOVA analyses.CC BY · PubMed Central

Figure 4 Quantitative comparisons of bacterial OTUs between the gut and biliary tract. Numbers in brackets denote OTU number discovered from each of four different types of samples, corresponding to four different colored boxes. Number in brackets located at the colored boxes denotes shared OTUs (at overlapped boxes) across either the four types of samples or those unique to a given sample type.CC BY · PubMed Central

Figure 5 Pipeline for identifying biliary tract core microbiome and potential microbial species associated with the presence of gallstones.CC BY · PubMed Central

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Authors: Wu, T., Zhang, Z., Liu, B., Hou, D., Liang, Y., Zhang, J., & Shi, P.
Affiliations: Kunming Institute of Zoology (CN)
First Affiliated Hospital of Kunming Medical University (CN)
Kunming Medical University (CN)
Corresponding author: Zhang, Jie
Shi, Peng
ORCID: Wu, Tao
Zhang, Zhigang
Liu, Bin
Zhang, Jie
Shi, Peng
Venue: BMC Genomics
Publisher: Springer Science and Business Media LLC
Published: 2013-10-01
Volume: 14
Issue: 1
Pages: 669-669
ISSN: 1471-2164 (ISSN-L)
DOI: 10.1186/1471-2164-14-669
PMC: PMC3851472
OpenAlex: W2116463764
Cited by: 234
References: 74
Citations by year: 2026: 13 · 2025: 20 · 2024: 29 · 2023: 29 · 2022: 29 · 2021: 29 · 2020: 19 · 2019: 17 · 2018: 15 · 2017: 10 · 2016: 12 · 2015: 9 · 2014: 3
FWCI: 3.58
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
Locations: BMC Genomics (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Funders: National Natural Science Foundation of China (31100916)
Chinese Academy of Sciences
Natural Science Foundation of Yunnan Province
Institute of Zoology, Chinese Academy of Sciences
Kunming Institute of Zoology, Chinese Academy of Sciences
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Health Sciences › Medicine › Gastroenterology › Gallbladder and Bile Duct Disorders
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords: cholesterol gallstones, gallstones, gut dysbiosis, bacterial community assembly, Proteobacteria, Faecalibacterium, Lachnospira, Roseburia, MDR genes
MeSH terms: Bacteria, Biliary Tract, Cholesterol, Female, Humans, Male, Middle Aged, Phylogeny, Gastrointestinal Tract, Gallstones, Metagenomics, Microbiota, Dysbiosis

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Gut microbiota dysbiosis and bacterial community assembly associated with cholesterol gallstones in large-scale study

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