A stable core gut microbiota across fresh- to saltwater transition for farmed Atlantic salmon

ABSTRACT

Gut microbiota associations through habitat transitions are fundamentally important, yet poorly understood. One such habitat transition is the migration from fresh to salt water for anadromous fish such as salmon. The aim of the current work was therefore to determine the fresh- to saltwater impact on the gut microbiota in farmed Atlantic salmon, with dietary interventions resembling that of fresh- and salt water diets with respect to fatty acid composition. Using deep 16S rRNA gene sequencing, and quantitative PCR, we found that the fresh- to salt water transition both had a major association with the microbiota composition and quantity, while diet did not show significantly associations with the microbiota. In salt water there was a 100-fold increase in bacterial quantity, with a relative increase of Firmicutes and a relative decrease of both Actinobacteria and Proteobacteria. Irrespective of an overall shift in microbiota composition from fresh to salt water we identified three core clostridia and one Lactobacillus-affiliated phylotype with wide geographic distribution that were highly prevalent and co-occurring. Taken together, our results support the importance of the dominating bacteria in the salmon gut, with the fresh water microbiota being immature. Due to the low number of potentially host associated bacterial species in the salmon gut, we believe farmed salmon can represent an important model for future understanding of host-bacterial interactions in aquatic environments.

IMPORTANCE

Little is known about factors affecting the inter-individual distribution of gut bacteria in aquatic environments. We have shown that there is a core of four highly prevalent and co-occurring bacteria irrespective of feed and fresh- to saltwater transition. The potential host interactions of the core bacteria, however, need to be elucidated further.