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 embryos 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 embryos are more susceptible to hyperlipidaemia when colonised with mouse high fat-diet-associated microbiota and that this effect can be driven by individual bacterial species. Colonisation or exposure to Enterococcus faecalis activates host Myd88 signalling, an effect that is phenocopied by the Gram positive Toll-like receptor agonists peptidoglycan and lipoteichoic acid, to drive hyperlipidaemia. In contrast, we find Stenotrophomonas maltophilia increases the hyperlipidaemic potential of chicken egg yolk independent of gut colonisation. In this work, we demonstrate the applicability of zebrafish as a tractable host for the identification of gut pathobionts via microbiota transplantation and subsequent challenge with a high fat diet.