The colours of the rainbow trout: Effects of feed and rearing conditions on gut microbial composition, metabolism, and product quality

A sustainable future for aquaculture depends on finding new feed sources, as
many issues with commercial ingredients can be alleviated using more sustainable alternatives. However, they must still uphold fish health, growth, and the final product quality. The gut microbiota is relevant here, as dietary changes may affect its composition, with further implications for the fish. The aim of this work was to assess the impact of alternative proteins on rainbow trout (Oncorhynchus mykiss) gut microbiota, liver and muscle metabolome, and the product quality. This work also aimed to deepen the understanding of gut microbial variation in commercial production systems and identify key variables influencing microbial composition. Five alternative protein sources were tested: black soldier fly (Hermetia illucens), mealworm (Tenebrio molitor), blue mussel (Mytilus edulis), tunicate (Ciona intestinalis), and a microfungus (Paecilomyces variotii). The tested protein sources clearly altered the digesta microbial communities, while growth and liver metabolite profiles remained largely stable. Muscle metabolite profiles showed clearer differences, but sensory differences were minor. Across commercial farms, gut microbial composition differed, with feed among the strongest explanatory factors, although the wider farm context also contributed. Moving fish from one facility to another altered the digesta microbiota even when the feed remained unchanged. The fish from two facilities also responded differently, suggesting that rearing- or host background shaped the responses. The subsequent feed change clarified the current diet as the strongest driver of digesta composition. Across the studies, digesta communities resembled feed microbiota more closely than water microbiota, and mucus-associated communities showed weaker responses and greater individual variation. Feed was the clearest driver of digesta microbiota, but responses were shaped by rearing context and host. These microbial changes did not correspond to changes in growth, metabolism, or product quality.