title: Differences in the biliary microbiome between biliary tract cancer and benign biliary disease
design: Differences in the biliary microbiome between biliary tract cancer and benign biliary disease
library_name: C088_p
library_construction_protocol: We enrolled 143 patients at Pusan National University Hospital between May 2021 and December 2023, including 56 patients diagnosed with BTCs and 87 with BBDs. A total of 84 patients were excluded because of their unsuitability for sequencing analysis. Clinical data and bile samples were collected during surgery or endoscopic retrograde cholangiopancreatography (ERCP). All bile samples obtained during ERCP were collected using a new catheter prior to the endoscopic sphincterotomy (EST) after guide wire-assisted cannulation only in cases in which the ampullary orifice was patented. Samples were aspirated using syringe suction before the administration of contrast agents. A minimum of 5 mL of bile was collected, and efforts were made to collect 10 mL or more whenever feasible. Fresh bile samples were immediately stored at -80°C after collection, 1 mL aliquots were divided into separate tubes for subsequent analysis. (IRB approval no. 2105-004-102) Frozen 1 mL bile juice sample were thawed, and microbiome DNA was extracted using the QIAamp DNA Microbiome Kit according to the manufacturer's instructions. The extracted microbiome DNA was eluted in 50 µL of the kit's elution buffer and stored at -20°C until further analysis. The V3–V4 regions of the 16S rRNA gene were PCR-amplified using barcoded universal primers. 