Effect of diets containing Hermetia illucens on rainbow trout microbiota: DGGE and NGS approaches

Hermetia illucens (Diptera: Stratiomydae; H) larvae are commonly studied as aquafeed ingredient due to their nutritional composition comparable to that of fishmeal. Different dietary formulations are reported to have different effects on fish gut microbiota, which, in turn, modulate fish digestion, immunity, energy balance, social behaviour and more. The previous studies reported contradictory results regarding the effect of insect-based diets on the microbiota of salmonids. Moreover, to the author’s knowledge, the effect of dietary full-fat insects on fish microbiota has not been addressed up to now. To fill the above-mentioned gap, the aim of this study was to elucidate the effect of a diet containing full-fat H larvae meal (H50, 50% substitution level of fishmeal with full-fat H larvae) on the gut microbiota of rainbow trout (Oncorhynchus mykiss) in comparison to a control diet containing fishmeal (H0). Microbial DNA from pyloric caeca mucosa (PC), pyloric intestine content (PIC), mid intestine mucosa (MI) and mid intestine content (MIC) from five fish samples per diet was extracted and subjected to denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (MiSeq, Illumina; HTS). Irrespective of the diet, the analysis of selected DGGE bands (excision, sequencing and closest relative search on BLASTN, NCBI) showed that the microbial communities were dominated by Bacillus sp. and Staphylococcus sp., with sparse Streptococcus sp., Mycoplasma sp. and Shigella sp. Bacterial relative abundances resulting from HTS analysis showed the domination of Proteobacteria in all samples (up to 85% relative abundance), followed by Firmicutes, Actinobacteria and Bacteroidetes. Fusobacteria were almost only found in MIC and PIC extracted from fish fed H0 diet. The differences between dietary groups were not captured by alpha-diversity (observed OTUs, Shannon’s entropy, Pielou’s evenness, tested with a Kruskal-Wallis test) or beta-diversity indices (unweighted unifrac, Jaccard, robust Aitchison metrics, plotted on PCoA and tested with a PERMANOVA). Further studies are needed to postulate a clearer hypothesis on the microbiota structure and diversity in fish fed dietary insects. That knowledge would pave the way to unravelling the functions of the microbiota and to understand the mechanistic laws at the root.