BackgroundSalmonids are important sources of protein for a large proportion of the human population. Interaction between the gut microbiota and host has in mammals been shown to affect the host phenotype, but relatively little is known about microbiota-host interaction in fish. Knowledge of microbiota-host interactions is of relevance for the aquaculture industry to achieve a more sustainable production by elucidating how microbes contribute to nutrition utilisation and immune responses of the fish host. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbial cells. Despite the reported dominance of intestinal Mycoplasma species, very little is known about their phylogenetic placement, functions and potential evolutionary relationships with their salmonid hosts. ResultsIn this study, we utilise 2.9 trillion metagenomic reads generated from 15 samples from three different salmonid host species to I) characterise and curate the first metagenome-assembled genomes (MAGs) of Mycoplasma dominating the intestines of three different salmonid species, II) establish the phylogeny of these salmonid candidate Mycoplasma species using known Mycoplasma genomes, III) perform a comprehensive pangenomic analysis of Mycoplasma, IV) decipher the putative functionalities of the salmonid MAGs and reveal specific functions expected to benefit the host. ConclusionOur results point to an established mutualistic relationship between Mycoplasma and its salmonid host species. Our data provide a basis for future studies examining the composition and function of the salmonid microbiota, with a potential for being further exploited in order to increase animal health and growth in aquaculture.