Diversity and composition of the gut microbiota of Atlantic salmon (Salmo salar) farmed in Irish waters

Aims Information on the gut microbiota of salmon is essential for optimizing nutrition while maintaining host health and welfare. This study’s objectives were to characterize the microbiota in the GI tract of Atlantic salmon (Salmo salar) farmed in waters off the west coast of Ireland and to investigate whether there is a difference in microbiota diversity between the proximal and distal regions of the intestine. Methods and Results The microbiota from the proximal and distal intestine (PI and DI, respectively) of Atlantic salmon was examined using MiSeq Illumina high‐throughput sequencing of the 16S ribosomal RNA gene. The PI region had greater bacterial diversity than the DI region. Six phyla were present in the DI samples, dominated by Tenericutes and Firmicutes. These six phyla were also amongst the 12 phyla detected in the PI samples. The PI microbiota was dominated by Tenericutes, Firmicutes, Bacteroidetes and Proteobacteria. A core microbiota of 20 operational taxonomic units (OTUs) common to both regions was observed. Conclusions It was concluded that Tenericutes were the dominant phylum in both PI and DI samples, and the PI region had greater Shannon and Simpson diversity of bacteria. However, further work is required to identify the functionality of the salmon microbiota. Significance and Impact of the Study Our study determined the composition and diversity of the intestinal microbiota in adult salmon from a commercial fishery and provides data to improve our understanding of their contributions to the nutrition, health and welfare of Atlantic salmon farmed in Irish waters.