Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish

Aims The aim of the present study was to investigate the composition of the intestinal microbiota during the acute stage of a bacterial infection to understand how dysbiosis of the gut may influence overall taxonomic hierarchy and diversity, and determine if there exists a bacterial taxon(s) that serve as markers for healthy or diseased rainbow trout (Oncorhynchus mykiss). Methods and Results From July to September 2015 29 specimens of three‐year‐old (an average weight from 240.9±37.7 to 850.7±70.1 g) rainbow trout Oncorhynchus mykiss were studied. Next‐generation high‐throughput sequencing of the 16S ribosomal RNA genes was applied to stomach and intestinal samples to compare the impact of infection status on the microbiota of rainbow trout Oncorhynchus mykiss (Walbaum) from the northwest part of Eurasia (Karelian region, Russia). The alpha diversity (Chao1, Simpson and Shannon index) of the microbial community of healthy rainbow trout was significantly higher than in unhealthy fish. The greatest contribution to the gut microbial composition of healthy fish was made by OTU's belonging to Bacillus, Serratia, Pseudomonas, Cetobacterium, and Lactobacillus. Microbiota of unhealthy fish in most cases was represented by the genera Serratia, Bacillus, and Pseudomonas. In microbiota of unhealthy fish there were also registered unique taxa such as bacteria from the family Mycoplasmataceae and Renibacterium. Analysis of similarities (ANOSIM test) revealed the significant dissimilarity between the microbiota of stomach and intestine (p≤0.05). Conclusions A substantial finding was the absence of differences between microbial communities of the stomach and intestine in the unhealthy groups if compared with healthy fish. Significance and Impact of Study These results demonstrated alterations of the gut microbiota of farmed rainbow trout, O. mykiss during co‐infections and can be useful for the development of new strategies for disease control programs.