A Bacterial-Sourced Protein Diet Induces Beneficial Shifts in the Gut Microbiome of the Zebrafish, Danio rerio
George B. H. Green, Michael B. Williams, Jeri L. Brandom, Sophie B. Chehade, Christian Fay, Casey D. Morrow, Addison L. Lawrence, Asim K. Bej, Stephen A. Watts
Abstract
BackgroundBacterial-sourced single cell proteins (SCPs) offer an alternative protein source for diet formulation for Zebrafish (Danio rerio) and other aquaculture models. In addition, the use of a single-cell bacterial protein source derived from multiple species, provides a unique insight into the interplay among nutrients in the diet, microbial populations in the diet, and the gut microbiome in D. rerio.Objective and MethodsWe investigated gut microbial compositions of D. rerio fed an open-formulation standard reference (SR) diet or a bacterial-sourced protein (BP) diet, utilizing microbial taxonomic co-occurrence networks, and predicted functional profiles.ResultsMicrobial communities in the SR diet were primarily composed of Firmicutes. In contrast, the BP diet was mainly composed of Proteobacteria. Alpha diversity revealed significant differences in microbial communities between the two diets, and between the guts of D. rerio fed either of the two diets. D. rerio fed with the SR diet resulted in a large abundance of Aeromonas and Vibrio. In contrast, D. rerio fed with BP diet displayed a large abundance of members from the Rhodobacteraceae family. Taxonomic co-occurrence networks display unique microbial interactions, and key taxon in D. rerio gut samples were dependent on diet and sex. Predicted functional profiling of the microbiome across D. Rerio fed SR or BP diets revealed distinct metabolic pathway differences. Female D. rerio fed the BP diet displayed significant upregulation of pathways related to primary and secondary bile acid synthesis. Male D. rerio fed the BP diet revealed similar pathway shifts and, additionally, a significant upregulation of polyketide sugar unit biosynthesis pathway.ConclusionThe use of a bacterial-sourced protein dramatically affects the composition and activity of the gut microbiome. Future investigations should further address the interplay among biological systems and diet, and may offer insights into potential health benefits in pre-clinical and translational animal models.