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Research article2024Peer reviewedOpen access

The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production

Gupta, Shashank; de Leon, Arturo Vera-Ponce; Kodama, Miyako; Hoetzinger, Matthias; Clausen, Cecilie G.; Pless, Louisa; Verissimo, Ana R. A.; Stengel, Bruno; Calabuig, Virginia; Kvingedal, Renate; Skugor, Stanko; Westereng, Bjorge; Harvey, Thomas Nelson; Nordborg, Anna; Bertilsson, Stefan; Limborg, Morten T.; Morkore, Turid; Sandve, Simen R.; Pope, Phillip B.; Hvidsten, Torgeir R.;
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Abstract

Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a priori mammalian microbiome knowledge on alpha-mannooligosaccharides (MOS) and beta-mannan-derived MDFs to study effects of such feed supplements in Atlantic salmon (Salmo salar) and their impact on its gut microbiome composition and functionalities. Our multi-omic analysis revealed that the investigated MDFs (two alpha-mannans and an acetylated beta-galactoglucomannan), at a dose of 0.2% in the diet, had negligible effects on both host gene expression, and gut microbiome structure and function under the studied conditions. While a subsequent trial using a higher (4%) dietary inclusion of beta-mannan significantly shifted the gut microbiome composition, there were still no biologically relevant effects on salmon metabolism and physiology. Only a single Burkholderia-Caballeronia-Paraburkholderia (BCP) population demonstrated consistent and significant abundance shifts across both feeding trials, although with no evidence of beta-mannan utilization capabilities or changes in gene transcripts for producing metabolites beneficial to the host. In light of these findings, we revisited our omics data to predict and outline previously unreported and potentially beneficial endogenous lactic acid bacteria that should be targeted with future, conceivably more suitable, MDF strategies for salmon.A multi-omic approach enables the reconstruction of microbial metabolic dynamics in the salmon gut in response to feed and feed supplements, outlining novel and potentially beneficial strategies to manipulate the salmon gut microbiota.

Published in

Communications biology
2024, volume: 7, number: 1, article number: 1391
Publisher: NATURE PORTFOLIO

SLU Authors

UKÄ Subject classification

Fish and Aquacultural Science

Publication identifier

  • DOI: https://doi.org/10.1038/s42003-024-07087-4

Permanent link to this page (URI)

https://res.slu.se/id/publ/139260