Title: The Salmon Microbial Genome Atlas (SMGA) enables novel insights into bacteria-host interactions via functional mapping
Abstract: The essential role of the gut microbiota for host health and nutrition is well established for many terrestrial animals, although its importance for fish and particularly Atlantic salmon is unclear. Here, we present the Salmon Microbial Genome Atlas (SMGA) originating from wild and farmed fish both in fresh and sea water, and consisting of 211 high-quality bacterial genomes, recovered by cultivation (n=131), gut metagenomics (n=77) and cell sorting (n=3). Bacterial genomes were taxonomically assigned into 16 different orders, including 32 distinctive genera and 31 potentially novel species. Testing the resource applicability of the SMGA demonstrated in vivo characterization of key populations in the salmon gut, with their ability to degrade diet-derived fibers and release vitamins and other exo-metabolites with known beneficial effects being validated via in vitro cultivation and metabolomics. Together, the SMGA facilitates high resolution functional insight into salmon gut microbiota with showcased application in a salmon nutrition context.