In the past decade, there has been an explosion of microbiome studies focused on the fish gut using next-generation sequencing (NGS) methods. Advances in the efficiency and affordability of DNA sequencing technologies have made it possible for researchers to identify over a thousand-fold higher number of microbes that would not be seen with previous culture dependent methods. There has been a particularly high number of NGS studies on the gut microbiome of farmed salmonid species, such as rainbow trout and Atlantic salmon, due to their importance to the aquaculture industry. Many studies have characterized the gut microbiome and have found certain bacteria phyla that dominate, such as Firmicutes, Proteobacteria and Actinobacteria, which commonly include beneficial bacteria Lactobacillus, Streptococcus and Corynebacterium spp. These bacteria and the larger community in the gut have been considered to be an “additional organ” due to their importance and ability to break down dietary fibre, produce short-chain fatty acids, synthesize vitamins, antagonize pathogens and interact with the immune system. Research is lacking on characterizing the gut microbiome of less commonly farmed salmonids, such as Arctic charr and coho salmon, although this may change is the future as they become more valuable to the industry. In addition, we are understanding more and more about environmental effects, such as temperature and rearing system, on the communities of gut bacteria in farmed fish.
There has been a recent shift from mapping the bacteria present in the gut of farmed fish to the specific affect of diet on these microbial communities, especially alternative protein and lipid sources used to replace the unsustainable inclusion of fishmeal and fish oil in the diet. Increased inclusion of plants (e.g. soy, corn and wheat), microbes (e.g. yeast, bacteria and microalgae) and insects (e.g. black soldier fly) have been found to influence the gut microbiome with dramatic changes at both the lower genus level and higher phyla level (Firmicutes:Proteobacteria ratio). Lower dietary inclusions or supplements of probiotics, prebiotics, organic acids and essential oils have also been found to modify the diversity and composition of the gut microbiome of farmed salmonids, albeit at a lower level (specific order or genus). I will present recent findings from several NGS studies that investigated dietary effects on the gut microbiome of salmonid fishes at the University of Guelph (Guelph, Canada), University of Stirling (Stirling, UK) and Swedish University of Agricultural Sciences (Uppsala, Sweden). The effects of these functional feed ingredients and increased replacement of fishmeal and fish oil with plants, microbes and insects on the gut microbiome will need to be optimized in the future to improve the nutrition, health and welfare of farmed salmonids and maintain the growth of the aquaculture industry.