Traditionally, the biliary tract has been considered to be normally sterile, and the presence of microorganisms in bile is a marker of a pathological process. This assumption was confirmed by failure in allocation of bacterial strains from the normal bile duct. The paper provides rationale for a phenomenon of the normal biliary microbiota as a separate functional layer which protects a biliary tract from colonization by exogenous microorganisms. We revealed the potential of metagenomic data for prevention of infectious diseases, post-operative complications of reconstructive interventions including bile duct stenting and implantation the tissue-engineered structures exposed to the risks of colonization with pathogenic / exogenous microorganisms. The methods based on preserving homeostasis of normal biliary microbiota ecosystem can be used for prevention of hepatobiliary diseases and treatment of biliary tract inflammatory diseases.