Gut dysbiosis is an important modifier of pathologies including cardiovascular disease but our understanding of the role of individual microbes is limited. Here, we have used transplantation of mouse microbiota into microbiota‐deficient zebrafish larvae to study the interaction between members of a mammalian high fat diet‐associated gut microbiota with a lipid rich diet challenge in a tractable model species. We find zebrafish larvae are more susceptible to hyperlipidaemia when exposed to the mouse high fat‐diet‐associated microbiota and that this effect can be driven by two individual bacterial species fractionated from the mouse high fat‐diet‐associated microbiota. We find Stenotrophomonas maltophilia increases the hyperlipidaemic potential of chicken egg yolk to zebrafish larvae independent of direct interaction between S. maltophilia and the zebrafish host. Colonization by live, or exposure to heat‐killed, Enterococcus faecalis accelerates hyperlipidaemia via host MyD88 signaling. The hyperlipidaemic effect is replicated by exposure to the Gram‐positive toll‐like receptor agonists peptidoglycan and lipoteichoic acid in a MyD88‐dependent manner. In this work, we demonstrate the applicability of zebrafish as a tractable host for the identification of gut microbes that can induce conditional host phenotypes via microbiota transplantation and subsequent challenge with a high fat diet.