We report the gut microbial composition, taxonomic co-occurrence networks, and predictive functional profiles of zebrafish, Danio rerio, fed a bacterial-based Single-Cell Protein diet (SCP) against a standard reference diet via targeted amplicon sequencing of the V4 region of the 16S rRNA gene. The microbial communities of SCP-fed D. rerio displayed increased abundances of Rhodobacter, Firmicutes ZOR0006, and Planctomycetia. In contrast, Vibrio and Aeromonas were dominant in the microbial community of D. rerio fed a standard reference diet. The co-occurrence network analysis revealed distinct differences amongst the microbial interactions in the SCP-fed and standard reference fed D. rerio. Taxonomic organizations in SCP-fed D. rerio were interconnected via Deinococcus and Ensifer and were determined as key taxa in the microbial network. In contrast, Rhizobiaceae and Rhodobacter were revealed to be key taxa in the standard reference diet. Predicted function of microbial community (PICRUSt2) of SCP-fed female D. rerio revealed significant upregulation in primary and secondary bile acid synthesis. The SCP-fed male revealed a significant upregulation in predicted metabolism attributes of xenobiotics by cytochrome P450. In contrast, the standard reference diet revealed an increase in cell-motility pathways. These data support future investigations to understand key interactions between the gut microbiome and diet, an essential component to maintain metabolic health in D. rerio, an important animal model of human disease.