The bile microbiome is a surrogate for the intratumoral microbiome in pancreatic ductal adenocarcinoma and is associated with oncological outcomes: a cohort study

Background: The bile microbiome has been shown to be associated with the development of pancreatic ductal adenocarcinoma (PDAC). However, the utility of bile fluid as a potential source of microbial biomarkers remains unknown. We aimed to characterize the bile microbial composition in PDAC compared to benign and malignant pancreatico–biliary disease, as well as correlate our findings with the pancreatic intratumoral and neighboring adjacent tissue (NAT) microbiome. Methods: Prospective matched pancreatic tumor, NAT, and bile samples were obtained from 54 patients who underwent surgery for a head of pancreas mass at Royal Surrey NHS Hospital Trust. Full-length 16S rRNA (V1-V9) gene sequencing was performed on the Oxford Nanopore MinION™ platform. The cohort consisted of 30 PDAC, 14 biliary tract cancers, and 10 benign cases. Results: We identified biliary microbial biomarkers Streptococcus (false discovery rate [FDR] = 0.0047) , Klebsiella (FDR = 0.0095) , Enterobacter (FDR = 9.68 × 10 −7 ), and Veillonella (FDR = 0.0140) that were found both in the bile and tumor in patients having surgery for PDAC. These bacterial genera were significantly more abundant in PDAC tumors compared to matched NAT and benign disease. We detected a negligible number of microbial reads in the NAT samples. Our microbial signature was highly predictive of PDAC within tissue (AUC = 0.9233) and bile (AUC = 0.8101). Positive bile cultures in the PDAC cohort increased the risk of deep-seated surgical site infections (SSIs), delayed gastric emptying, and post-operative pancreatic fistula. Biliary stenting did not affect microbial composition, and the abundance of specific genera significantly correlated with overall survival and disease-free survival in PDAC. Conclusion: We have shown that the normal pancreas is a relatively sterile organ, whilst the PDAC tumor and bile are colonized with specific genera. In fact, 71% of the tumor microbiome is shared with the bile microbiome in PDAC, suggesting that bile may serve as a potential future diagnostic and prognostic microbial biomarker as well as a surrogate readout of the tumor microbiome. The function of these microbes during pancreatic tumorigenesis remains to be determined. Furthermore, intra-operative biliary culture may serve as a low-cost predictor of post-operative outcomes.