Microbiota studies in the bile duct strongly suggest a role for Helicobacter pylori in extrahepatic cholangiocarcinoma

Abstract

Biliary tract cancer or extrahepatic cholangiocarcinoma (ECCA) represents the sixth commonest cause of cancer in the gastrointestinal tract in western countries. We aimed to characterize the microbiota and its predicted associated functions in the biliary tract of ECCA and benign biliary pathology (BBP). Samples were taken from 100 patients with ECCA and 100 patients with BBP by endoscopic cholangio-pancreatography for DNA extraction. Ten patients with ECCA and ten with BBP were selected for microbiota studies using the V4-16S rRNA gene and sequenced in Illumina platform. Microbiota analyses included sample-to-sample distance metrics, ordination/clustering and prediction of functions. Presence of Nesterenkonia sp. and Helicobacter pylori cagA and vacA genes were tested in the 100 ECCA and 100 BBP samples. Phylum Proteobacteria dominated all samples (60.4% average). Ordination multicomponent analyses showed significant microbiota separation between ECCA and BBP (p 0.010). Analyses of 4002 operational taxonomic units with presence variation in at least one category probed a separation of ECCA from BBP. Among these, Nesterenkonia decreased, whereas Methylophilaceae, Fusobacterium, Prevotella, Actinomyces, Novosphingobium and H. pylori increased in ECCA. Predicted associated functions showed increased abundance of H. pylori virulence genes in ECCA. cagA and vacA genes were confirmed by PCR in ECCA and BBP samples. This is the first microbiota report in ECCA and BBP to show significant changes in microbial composition. Bacterial species unusual for human flora were found: Methylophilaceae and Nesterenkonia are reported in hypersaline soils, and Mesorhizobium is a nitrogen-fixing bacterium. Enrichment of virulence genes confirms previous studies suggesting that H. pylori might be associated with ECCA.

Chronic Opisthorchis viverrini Infection Changes the Liver Microbiome and Promotes Helicobacter Growth

“…Bacterial infection has previously been implicated in hepatobiliary diseases (HBDs) in human [12, 31] and hamster tissues [32]. Boonyanugomol et al have identified H .…”

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes

“…Sample DNA was extracted and quantified as described previously [9] for human oral biopsy samples and for rat fecal samples [13]. Amplification of the V4 region of the 16S rRNA was performed with the 515F and 806R bacterial universal primer set with attached Illumina sequencing adaptor (Illumina, San Diego, CA).…”

“…Amplification of the V4 region of the 16S rRNA was performed with the 515F and 806R bacterial universal primer set with attached Illumina sequencing adaptor (Illumina, San Diego, CA). Amplified products were sequenced using Illumina MiSeq instrument as described previously [13]. …”

“…To pre-process 16S rRNA gene libraries for Piphillin functional inference, sequences were binned into OTUs, a representative sequence from each OTU was selected and the count of sequences in each OTU from each sample were tallied using a previously described method [13]. …”

The Possible Role of Helicobacter pylori Infection in Non-alcoholic Fatty Liver Disease

“…The authors speculated two possible mechanisms for the presence of H. pylori in the liver: the bacterium may pass from the stomach to the liver through the duodenum and biliary tract, or may arrive in the liver from the circulation through the hepatic portal vein (Pellicano et al, 2008). Some data indicate the biliary pathway as the most plausible route (Tiwari et al, 2006; Aviles-Jimenez et al, 2016). …”