The gut microbiota of healthy and Flavobacterium psychrophilum-infected rainbow trout fry and the effect of antibiotics and phage therapies

In the aquaculture sector, there is an increased interest in developing environmentally friendly alternatives to antibiotics in the treatment and prevention of bacterial infections. In this study, we focused on the freshwater pathogen Flavobacterium psychrophilum and investigated the effects of antibiotics (florfenicol) and phage therapies on the gut microbiota of healthy and infected rainbow trout fry (1-2 g). Florfenicol-coated feed was administered for 10 days starting two days after the infection procedure. A two component mix of phage targeting F. psychrophilum (FpV4 and FPSV-D22) was continuously delivered by feed with a prophylactic period of 12 days. Samples of the distal intestine were collected over time (day -1 and 1, 8 and 33 days post infection) and analyzed by community analysis targeting the 16S rRNA gene (V3-V4 region).