The Salmon Microbial Genome Atlas enables novel insights into bacteria-host interactions via functional mapping
de Leon, A. V.-P.; Hoetzinger, M.; Hensen, T.; Gupta, S.; Weston, B.; Johnsen, S. M.; Rasmussen, J. A.; Clausen, C. G.; Pless, L.; Verissimo, A. R. A.; Rudi, K.; Snipen, L. G.; Karlsen, C. R.; Limborg, M. T.; Bertilsson, S.; Thiele, I.; Hvidsten, T. R.; Sandve, S. R.; Pope, P. B.; La Rosa, S. L.
Show abstract
The essential role of the gut microbiota for host health and nutrition is well established for many terrestrial animals, while 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 freshwater and seawater, and consisting of 211 high-quality bacterial genomes, recovered by cultivation (n=131) and gut metagenomics (n=80). Bacterial genomes were taxonomically assigned into 14 different orders, including 28 distinctive genera and 31 potentially novel species. Benchmarking the SMGA, we functionally characterized key populations in the salmon gut that were detected in vivo. This included the ability to degrade diet-derived fibers and release vitamins and other exo-metabolites with known beneficial effects, which were validated by in vitro cultivation and untargeted metabolomics. Together, the SMGA enables high resolution functional insight into salmon gut microbiota with relevance for salmon nutrition and health.
Matching journals
The top 4 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia 96%
- Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation 96%
- Single-colony sequencing reveals phylosymbiosis, co-phylogeny, and horizontal gene transfer between the cyanobacterium Microcystis and its microbiome 96%
Similar papers in this journal
Similar papers in this journal
- Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean 96%
- Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation 96%
- Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species 96%
Similar papers in this journal
- Longitudinal, Multi-platform Metagenomics Yields a High-quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities 97%
- BiG-MAP: an automated pipeline to profile metabolic gene cluster abundance and expression in microbiomes 95%
- Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes 95%
Similar papers in this journal
- Bacteria Contribute Exopolysaccharides to an Algal-Bacterial Joint Extracellular Matrix 95%
- Microbiome-Dependent Functional Responses to Structurally Distinct Oligosaccharides Revealed by Metaproteomics 95%
- Disturbance-based management of ecosystem services and disservices in partial nitritation anammox biofilms 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.