High-throughput sequencing of gut microbiota in rainbow trout (Oncorhynchus mykiss) fed larval and pre-pupae stages of black soldier fly (Hermetia illucens)

Black soldier fly (Hermetia illucens) meal is a potential alternative to fishmeal and plant proteins in diets for farmed fish since it can be produced on organic waste substrates, requires little energy and water inputs and contains high levels of essential amino acids. Recent studies have partially replaced fishmeal with black soldier fly meal, however, research on their impact on gut microbiota of fish is limited. In a five week experiment, juvenile rainbow trout (Oncorhynchus mykiss) were fed either a reference diet based on fishmeal or three diets with 30% inclusion of black soldier fly meals in the form of pre-pupae, larvae or defatted-larvae. The combined luminal content and mucosa were collected from the distal intestine of three fish per tank with four tanks per diet (n = 12) and 16S rRNA gene amplicons were sequenced using the Illumina MiSeq platform. Feeding the insect-based diets increased the alpha-diversity of bacteria and abundance of lactic acid bacteria, which may be due to the addition of dietary chitin. Compared with fishmeal, feeding insects resulted in higher abundance of phyla Firmicutes and Actinobacteria with lower abundance of Proteobacteria. Fish fed the full-fat meals had higher abundance of Corynebacterium that was attributed to its ability to produce lipase and the high content of dietary lipids as a substrate. Bacillaceae was increased in fish fed both larvae diets and unchanged in the pre-pupae diet, which indicated that life-cycle stage of the insect influenced the gut microbiota. Based on these results, we found that feeding black soldier flies increased diversity and altered the composition of gut bacteria of rainbow trout, which were further influenced by life-cycle stage and lipid content of the insect meal.