SalmoSim: the development of a three-compartment in vitro simulator of the Atlantic Salmon GI tract and associated microbial communities

Abstract BackgroundAtlantic salmon are a fish species of major economic importance. Innovative strategies are being sought to improve salmon feeds and feed additives to enhance fish performance, welfare, and the environmental sustainability of the aquaculture industry. There is still a lack of knowledge surrounding the importance and functionality of the salmon gut microbiome in fish nutrition. In vitro gut model systems might prove a valuable tool to study the effect of feed, and additives, on the host’s microbial communities. Several in vitro gut models targeted at monogastric vertebrates are now in operation. Here, we report the development of an Atlantic salmon gut model, SalmoSim, to simulate three gut compartments (stomach, pyloric caecum and midgut) and associated microbial communities. ResultsThe gut model was established in a series of linked bioreactors seeded with biological material derived from farmed adult marine phase salmon. In biological triplicate, the response of the in vitro system to two distinct dietary formulations (fish meal and fish meal free) was compared to a parallel in vivo trial over forty days. Metabarcoding based 16S rDNA sequencing, qPCR, ammoniacal nitrogen and volatile fatty acid measurements were undertaken to survey the microbial community dynamics and function. SalmoSim microbiomes were indistinguishable (p=0.230) from their founding inocula at 20 days and the most abundant genera (e.g. Psycrobacter, Staphylococcus, Pseudomonas) proliferated within SalmoSim. Real salmon and SalmoSim responded similarly to the introduction of novel feed, with majority of the taxa (96% Salmon, 97% SalmoSim) unaffected, while a subset of taxa (e.g. a small fraction of Psychrobacter) were differentially affected across both systems. Consistent with a low impact of the novel feed on microbial fermentative activity, volatile fatty acids profiles were not significantly different in SalmoSim pre- and post-feed switch.ConclusionThis study represents an important step in the development of an in vitro gut system as a tool for the improvement of salmon nutrition and welfare. This system aims to be utilised as a pre-screening tool for new feed ingredients and additives, as well as being used to study antimicrobial resistance and transfer, and fundamental ecological processes that underpin microbiome dynamics and assembly.