The salmon microbial genome Atlas enables novel insights into bacteria host interactions via functional mapping
The essential role of the gut microbiota for host health and nutrition is well established for humans and many terrestrial animals, although its importance for fish and particularly Atlantic salmon, is unclear. This knowledge gap restricts development of dietary interventions to promote fish growth and disease resilience and is predominately driven by a paucity of salmon gut-derived microbial genomes. Here, we present the Salmon Microbial Genome Atlas (SMGA), a collection of cultured and uncultured bacteria from the salmon gut, originating from wild and farmed fish both in fresh and sea water. The SMGA consists of 233 high-quality bacterial genomes, recovered by metagenomics (n=99), cell sorting (n=3) and cultivation (n=131) using both short and long-read sequencing. Bacterial genomes were taxonomically assigned into 23 different orders, including 28 unique genera and 66 potentially novel bacterial species. The resource applicability of the SMGA was demonstrated via the mapping of metatranscriptomic data derived from a salmon trial, which enabled reconstruction of active metabolic pathways from key Enterobacterales and Pseudomonadales populations in the salmon gut. To validate omic-based predictions both populations were pursued by in vitro cultivation and untargeted metabolomics, which confirmed their metabolism of diet-derived fibers such as chitin, cello-oligosaccharides and manno-oligosaccharides, and their release of vitamins and other exo-metabolites with known beneficial effects in the salmon gut. Together, the SMGA facilitates high resolution insight into both species diversity and function of the salmon gut microbiota with showcased application in a salmon nutrition context.