Intestinal bacterial community structure differs between healthy and inflamed intestines in Atlantic salmon (Salmo salar L.)

•Bacterial population of healthy and inflamed intestines was evaluated.•The use PCR-DGGE allows screening of changes in the intestinal bacterial community.•The bacterial community differs between healthy and inflames intestines.•SBM diet gave increased relative abundance of Firmicutes bacteria in the distal intestine.•Intestinal bacteria could play a role in the SBM-induced enteritis.

Atlantic salmon (Salmo salar L.) fed soybean meal (SBM) are known to develop SBM-induced enteritis with atrophy of intestinal folds and inflammation in the lamina propria. In this study, intestinal contents of mid (MI) and distal intestine (DI) were collected from 12 fish fed one of the following diets for 80 days: a fish meal (FM) diet and SBM diet. Polymerase chain reaction denaturing gradient gel electrophoresis analysis of 16S ribosomal ribonucleic acid gene was used to evaluate whether changes in bacterial population were associated with healthy and inflamed intestines. Fish fed the same diet were mainly clustered together in both MI and DI. The diversity indices were strongly reduced by the SBM diet in DI, as shown by both richness and Shannon–Weaver indices. The SBM diet gave a higher relative abundance of Firmicutes bacteria than the FM diet in the DI. The most dominant species were Lactococcus lactis subsp. lactis, Weissella confusa, and Photobacterium phosphoreum. To conclude, the intestinal bacterial population was highly affected by dietary conditions and might play a role in the development of SBM-induced enteritis.