Influence of the Biliary System on Biliary Bacteria Revealed by Bacterial Communities of the Human Biliary and Upper Digestive Tracts

Abstract

Biliary bacteria have been implicated in gallstone pathogenesis, though a clear understanding of their composition and source is lacking. Moreover, the effects of the biliary environment, which is known to be generally hostile to most bacteria, on biliary bacteria are unclear. Here, we investigated the bacterial communities of the biliary tract, duodenum, stomach, and oral cavity from six gallstone patients by using 16S rRNA amplicon sequencing. We found that all observed biliary bacteria were detectable in the upper digestive tract. The biliary microbiota had a comparatively higher similarity with the duodenal microbiota, versus those of the other regions, but with a reduced diversity. Although the majority of identified bacteria were greatly diminished in bile samples, three Enterobacteriaceae genera (Escherichia, Klebsiella, and an unclassified genus) and Pyramidobacter were abundant in bile. Predictive functional analysis indicated enhanced abilities of environmental information processing and cell motility of biliary bacteria. Our study provides evidence for the potential source of biliary bacteria, and illustrates the influence of the biliary system on biliary bacterial communities.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1. Distribution of genera that were highly prevalent across the four body sites.

Only genera with ≥0.01% abundance in at least 12 samples are presented. OTUs that could not be assigned at the genus level were labelled as “unclassified” (uncl.). Genera that were poorly defined in Greengenes database were labelled as “other”. [Prevotella] and [Mogibacteriaceae] are provisional taxonomical assignments of operational taxonomic units by Greengenes. The upward and downward arrows indicated genera whose abundance was increased and decreased in bile samples, relative to the other regions, respectively.

Fig 2. Correlation coefficients between the microbiota of each upper digestive tract site and the biliary microbiota.

For each patient, correlation coefficients between the microbiota of the biliary tract and other sampling sites were calculated when Pyramidobacter and three Enterobacteriaceae genera (Escherichia, Klebsiella, and an unclassified genus) in bile samples were included (a) and excluded (b). Saliva, gastric fluid, duodenal fluid, and bile are denoted as “S”, “G”, “D”, and “B”, respectively, on the x-axis. Correlations that were statistically significant are indicated with red circles.

Fig 3. Distribution of differentially abundant genera among all sampling sites.

Genera were filtered by the criteria of with a ≥10% abundance in at least one sampling site and with a ≥0.01% abundance in at least 12 samples. Then, filtered genera that were decreased (a) and increased (b) in relative abundance in bile samples compared to at least one of the other body sites were illustrated. The y-axis represents relative abundance. Body sites that showed statistically significant differences relative to bile samples are labelled with an “*”. Boxes represent the 25th- to 75th-percentile interquartile range. The red lines inside the boxes indicate the median values, and the whiskers represent the most extreme values within 1.5 times of the interquartile range. Red lines for genus Pyramidobacter have been especially thickened for a better visualization as the median values were close to zero. Outlier values are represented as circles. **P < 0.01, *P < 0.05.

Fig 4. Bacterial metabolic pathways of saliva, gastric fluid, duodenal fluid, and bile samples.

KEGG pathways with higher (a) and lower (b) abundance in bile samples, relative to the other sites, were illustrated. Body sites with significant differences relative to bile samples are labelled with an “*” (P < 0.05) or “#” (P < 0.01) above the bars.