Microbiome diversity and dysbiosis in aquaculture

Abstract

With the continuous growth of the human population and associated need for high‐quality protein, the aquaculture sector will be required to increase significantly in productivity. This growth in productivity will be achieved through more efficient use of resources like feeds, genetic improvement and limiting the impacts of disease. One of the key links between animal productivity and disease is that of microbial diversity, with high‐throughput sequencing technologies increasing our understanding of the role microorganisms play in health, development and physiology of vertebrate and invertebrate hosts alike. Increasing our understanding of microbial–host interactions will help avoid or manage dysbiosis in aquaculture systems with the final aim of improving productivity. We review the current literature, which indicates that there is an association between productivity and microbial diversity in aquaculture systems, as changes in bacterial microbiomes are implicated in animal performance, in disease development associated with both bacterial and viral origin, and in dysbiosis triggered by environmental stressors or diet choice. Dysbiosis, whether in the form of the loss of beneficial bacteria, or the expansion of pathogens or potentially harmful microorganisms, can be used as an indicator tool for productivity monitoring purposes. Development of management strategies towards preserving the microbial balance, including maintaining or increasing diversity in the host, is critical for the health of cultured aquatic animals and will likely be critical for the expansion of aquaculture.

Robust host source tracking building on the divergent and non-stochastic assembly of gut microbiome in wild and farmed large yellow croaker

“…Lastly, although it is not the major aim of the present study, understanding the underlying mechanisms responsible for the divergence of gut microbiome between the wild and farmed fishes can also provide key information on improving production of aquaculture [21]. Dysbiosis has been widely reported in the aquaculture fishes fed with formulated feed [79]. Our study revealed possible dysbiosis in farmed croaker since potential pathogenic bacterial taxa, such as Vibrio spp., Photobacterium spp.…”

Interaction Between Dietary Lipid Level and Seasonal Temperature Changes in Gilthead Sea Bream Sparus aurata: Effects on Growth, Fat Deposition, Plasma Biochemistry, Digestive Enzyme Activity, and Gut Bacterial Community

“…The study of the gut microbiota has received great attention in the aquaculture sector as an indicator of productivity and fish health, and it is likely that its manipulation will be achieved in the near future in several fish species of commercial interest. Several studies have recently addressed the effect of diet (Huyben et al, 2020;Rimoldi et al, 2020), rearing density (Parma et al, 2020), age, sex (Piazzon et al, 2019), and genetic background (Piazzon et al, 2020) on the gut microbiota of gilthead sea bream; however more studies to detect dynamical changes of microbial composition during the farming cycle are necessary (Infante-Villamil et al, 2020). In the present study, at high phylogenetic levels, the overall gut microbiome structure was similar among groups, and the main represented taxa at phylum (Firmicutes, Proteobacteria, and Actinobacteria) and family (Lactobacillaceae) levels are consistent with previous trials on this species reared on similar aquafeed formulation and feeding protocols (Parma et al, 2016(Parma et al, , 2020.…”

Effects of phytonutrient-supplemented diets on the intestinal microbiota of Cyprinus carpio

“…The GIT microbiome composition shapes host physiology and growth, but these functions in aquatic animal hosts have not yet been fully investigated. Only a limited number of studies have evaluated the association between the fish microbiota and production outcomes in aquaculture settings [ 66 , 67 ].…”