Abstract
BackgroundThe aquaculture sector now accounts for almost 50% of all fish for human consumption and is anticipated to provide 62% by 2030. Innovative strategies are being sought to improve fish 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 teleost 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. We first aimed to achieve a stable microbiome composition representative of founding microbial communities derived from Atlantic salmon. Then, in biological triplicate, the response of the in vitro system to two distinct dietary formulations (fishmeal and fishmeal free) was compared to a parallel in vivo trial over 40 days. Metabarcoding based on 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 (OTUs accounting for 98% of all reads shared with founding communities). 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) was differentially affected across both systems. Consistent with a low impact of the novel feed on microbial fermentative activity, volatile fatty acid profiles were not significantly different in SalmoSim pre- and post-feed switch.ConclusionBy establishing stable and representative salmon gut communities, this study represents an important step in the development of an in vitro gut system as a tool for the improvement of fish nutrition and welfare. The steps of the system development described in this paper can be used as guidelines to develop various other systems representing other fish species. These systems, including SalmoSim, aim to be utilised as a prescreening 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.8JdHojFsA4Kj53z48mRJ2PVideo abstract
Highlights
The aquaculture sector accounts for almost 50% of all fish for human consumption and is anticipated to provide 62% by 2030
Stabilisation of representative microbial communities within the SalmoSim system Effective richness (Fig. 2A) indicates that within the stomach and midgut compartments, the initial inoculum contained the highest number of operational taxonomic units (OTUs) compared with later sampling time points from the SalmoSim system: in the stomach compartment, effective richness was statistically different between time point 0 and time points 18, 30, 36, and 38, and within the midgut compartment, the number of OTUs within the initial inoculum was statistically different from time points 2, 4, 6, 16, 34, 36, 38, and 40
Comparison of non-inoculum salmon and SalmoSim samples at the microbial level showed significant differences using both ecological and phylogenetic metrics as well as a different number of OTUs (SalmoSim 508 OTUs and real salmon samples 192 OTUs). These differences may be explained by the fact that samples used for non-inoculum salmon and SalmoSim originated from different individuals, whereas initial inoculum and SalmoSim samples for a given run originated from the same fish
Summary
The aquaculture sector accounts for almost 50% of all fish for human consumption and is anticipated to provide 62% by 2030. Innovative strategies are being sought to improve fish feeds and feed additives to enhance fish performance, welfare, and the environmental sustainability of the aquaculture industry. In vitro gut model systems might prove a valuable tool to study the effect of feed, and additives, on the host’s microbial communities. In the last 50 years, per capita fish consumption has almost doubled from 10 kg in the 1960s to over 19 kg in 2012 [1]. This increase in the demand for fish protein has put wild fish stocks under pressure. To improve aquaculture environmental and financial sustainability, the ratio of the marine origin components (Fishmeal (FM) and Fish Oil (FO)) within feeds has reduced considerably. In Norway the ratio of the marine origin components within farmed salmon feed reduced from around 90% in 1990 to 30% in 2013 [6]
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