Effect of diet-induced intestinal inflammation on the gut microbiome and transcriptome in a model teleost

Background/Question/Methods

Historically, fishmeal (FM) was the major protein dietary source used in the aquaculture industry. Material shortages and environmental pressures have led to considerable research on replacements. Due to its high availability and low cost, soybean meal (SBM) has become the most commonly used protein source, despite growing evidence that differing replacement amounts of SBM negatively impacts fish health in many species. We compared the impact of a 50% SBM replacement vs a 100% FM diet on intestinal morphology, and the gut microbiome and transcriptome in a model teleost, Japanese medaka (Oryzias latipes), in two age classes. Young (3-month) and old (15-month) fish were fed SBM or FM for 2-week or 4-weeks, while the old cohort were also fed a standard vivarium diet (STD), which contained components of both SBM and FM. Long-read sequencing was performed on an Oxford Nanopore MinION™ Mk1B to assess differences in i) microbial diversity based on full-length 16S rRNA reads or ii) global gene expression (i.e. transcriptome) based on full-length mRNA’s (PCR-mRNA) analysis. Differences in gene expression for genes of interest (GOI) were also assessed using qRT-PCR.

Results/Conclusions

Significant histological changes were observed in the intestines of fish fed SBM for 2-weeks. Goblet cell number decreased and the width of the lamina propria increased. No differences were observed in microbial alpha-diversity (Shannon’s Index, Pielou’s Evenness), but fish fed the STD diet had a higher Firmicutes:bacteria and a lower Proteobaterica:bacteria ratio. Despite this shift, no diet was concluded to have a ‘healthier’ microbiome because the intestinal microbiome of teleosts is not well defined. Analyses of the expression of gut peptide hormones using qRT-PCR found significant differences in the expression of genes (e.g. pyy, gcg, insl5) associated with metabolic shifts; global transcriptomic analysis is underway. The utility of the MinION™ Mk1B for studying shifts in the fish microbiome and transcriptome is discussed. Taken together, we find evidence that a 50% SBM replacement induced intestinal inflammation in Japanese medaka.