Hötzinger, Matthias
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
- Norwegian University of Life Sciences (NMBU)
Research article2024Peer reviewed
Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health
de Leon, Arturo Vera-Ponce; Hensen, Tim; Hoetzinger, Matthias; Gupta, Shashank; Weston, Bronson; Johnsen, Sander M.; Rasmussen, Jacob A.; Clausen, Cecilie Gronlund; Pless, Louisa; Verissimo, Ana Raquel Andrade; Rudi, Knut; Snipen, Lars; Karlsen, Christian Rene; Limborg, Morten T.; Bertilsson, Stefan; Thiele, Ines; Hvidsten, Torgeir R.; Sandve, Simen R.; Pope, Phillip B.; La Rosa, Sabina Leanti
Abstract
To ensure sustainable aquaculture, it is essential to understand the path 'from feed to fish', whereby the gut microbiome plays an important role in digestion and metabolism, ultimately influencing host health and growth. Previous work has reported the taxonomic composition of the Atlantic salmon (Salmo salar) gut microbiome; however, functional insights are lacking. Here we present the Salmon Microbial Genome Atlas consisting of 211 high-quality bacterial genomes, recovered by cultivation (n = 131) and gut metagenomics (n = 80) from wild and farmed fish both in freshwater and seawater. Bacterial genomes were taxonomically assigned to 14 different orders, including 35 distinctive genera and 29 previously undescribed species. Using metatranscriptomics, we functionally characterized key bacterial populations, across five phyla, in the salmon gut. This included the ability to degrade diet-derived fibres and release vitamins and other exometabolites with known beneficial effects, which was supported by genome-scale metabolic modelling and in vitro cultivation of selected bacterial species coupled with untargeted metabolomic studies. Together, the Salmon Microbial Genome Atlas provides a genomic and functional resource to enable future studies on salmon nutrition and health.Using shotgun metagenomics, cultivation and metabolic modelling, the authors construct the Salmon Microbial Genome Atlas as a resource for future studies on sustainable aquaculture.
Published in
Nature microbiology
2024, volume: 9, number: 11, pages: 3059-3074
Publisher: NATURE PORTFOLIO
SLU Authors
Bertilsson, Stefan
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
UKÄ Subject classification
Fish and Aquacultural Science
Microbiology
Publication identifier
- DOI: https://doi.org/10.1038/s41564-024-01830-7
Permanent link to this page (URI)
https://res.slu.se/id/publ/133039