The aquaculture microbiome

A more productive and sustainable aquaculture sector is needed to meet sustainable development goals and supply a growing world population with high-quality protein. The industry is faced with the challenge to significantly increase productivity while at the same time securing both livelihoods and sustainability.

Controlling the microorganisms that are associated with aquaculture systems (i.e. the aquaculture microbiome) has always been essential in high-intensity rearing of fish. Disease outbreaks caused by pathogenic bacteria are believed to be one of the most serious challenges faced by the aquaculture industry, and consequently, extensive measures are taken to limit the introduction and proliferation of such bacteria in the aquaculture systems. Furthermore, microbial activity in these naturally eutrophied systems may produce unwanted toxic metabolites such as hydrogen sulphide, which is formed when microorganisms reduce sulphate in anaerobic respiration and which interferes with mammalian respiration.

However, microbes may also serve as a solution to an array of these very challenges. In the agriculture industry, microbiome-based products such as seed coatings that increase nutrient uptake in crops, and which antagonize plant pathogenic soil organisms, are becoming increasingly popular tools to improve productivity in a sustainable manner, and microbiome-based products may reach a market size comparable to that of chemical agro-chemicals within a few years.

Microbiome analysis solutions for the aquaculture industry

In the aquaculture industry, fish are traditionally kept in high densities in a medium that facilitates the transfer of microbes. The microbiome is seen as an integral part of keeping fish raised for food healthy and productive. Maintaining a healthy microbiome in fish is particularly important for closed recirculating agriculture systems, however open systems in which there is potential transfer of microbes between captive and wild populations, and waste from kept fish must be managed also benefit from managing the fish microbiome.

The link between the gut microbiome and immunity has been well established in fish. A diverse microbiome is beneficial to prevent infection by pathogens for several reasons. Lactobacillus and Bacillus are both used as probiotics in aquaculture because they improve the fish gut barrier function and the germ-fighting abilities of the fish immune system.Antibiotics are used in aquaculture to control pathogens, however they can have profound and long-lasting effects on the fish microbiome that leads to a decrease in productivity. By measuring gut microbiome changes, the effects of interventions on the microbiome after the use of antibiotics can be tracked.

BaseClear offers niche microbiome analysis solutions, including for aquaculture microbiome analysis. BaseClear offers complete aquaculture microbiome analysis and reporting services for better insights of microbial populations and their functions. BaseClear is involved in several projects that are focused on this emerging research area to identify and characterize the microbiomes of various aquaculture species.

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