Infection and antibiotic treatment have prolonged effects on gut microbiota, muscle and hepatic fatty acids in rainbow trout (Oncorhynchus mykiss).

Our results demonstrated that infectious disease and antibiotic treatment of reared species can cause a pertinent imbalance in their gut microbiota and reduce the abundance of specific fatty acids. This can be useful for the sustainable aquaculture industry due to the development of early indication technologies for rapid disease diagnosis.