Influence of environmental and host factors on the gut microbiome and lipid metabolism in salmonid fishes

Last changed: 13 April 2021
Two annual salmon on a table, one smolted and one unsmolted. Photo.

The goal is to improve our understanding of the environmental impact and influence of host animal factors on intestinal microbiota and lipid metabolism in salmon.

Climate change, pollution and growing food demand continue to increase stress on the health and production of wild and farmed salmon. Recent evidence has shown that different profiles of lipids and fatty acids in salmonid fishes can influence their migration success, immune status and metabolic rate. Gut microbes play a role in providing short-chain fatty acids and other essential nutrients for animals, although research is lacking on the microbial contribution to fish and influences from the diet and host genetics.

The overall aim of this project is to identify how the gut microbiome influences lipid metabolism under varying conditions and the resulting health effects on salmon. To address this aim the following objectives are to:

1) perform a meta-analysis to rank factors influencing the salmon gut microbiome

2) quantify nutrients produced from microbes in an artificial fish gut system (ex vivo)

3) determine dietary impacts of feeding probiotics on gut integrity and microbiota of farmed salmon (in vivo)

4) identify life-stage and genetic effects on gut microbiome of wild salmon (in vivo).

In addition to nutritional analyses, the Illumina next-generation sequencing platform (NGS) will be used to identify gut microbes (16S and 18S rRNA) and to genotype markers (SNP chip).

This study will combine expertise from SLU, Gothenburg’s University and, Guelph University, Canada to improve our understanding of environmental and host influences on the gut microbiome and lipid metabolism of salmon.


The project is financed by Formas and runs between 2021-2024.

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