Opportunities for microbiome research to enhance farmed freshwater fish quality and production

Freshwater fish farming is the largest sub-sector of the global aquaculture industry, with its continued success dependent on the industry's ability to be productive and sustainable. In recent years, microorganisms have been increasingly recognised for their role in the health and overall performance of aquatic organisms, providing the aquaculture industry with a promising avenue for further success. Here, we review the literature on freshwater fish microbiology to evaluate the potential for microbial research to enhance freshwater aquaculture. A systematic review revealed that the existing freshwater fish microbiology literature incorporates <1% of freshwater fish species, with most studies focussed on Cyprinidae, Salmonidae and to a lesser extent Cichlidae. Using social network analyses, this review identified 25 key research areas commonly addressed in the existing literature highlighting the narrow focus of existing studies. Microbial community structure was the most frequently researched area, followed by environment and diet. These studies often evaluated microbiota changes associated with diadromous migrations, new technologies and advancements in feed formulations. However, research areas, such as the role of microorganisms in fish fecundity, omega-3 content, sustainability and palatability, were underrepresented in the literature despite their influence on aquaculture success. These underrepresented research areas are examples of where additional investments in microbial research are needed to ensure the continued expansion and success of freshwater aquaculture.

Automated summary

Freshwater fish farming is the largest sub-sector of the global aquaculture industry, with microbial research holding potential to further enhance the industry's success. However, existing literature on freshwater fish microbiology covers less than 1% of freshwater fish species, with a narrow focus on certain fish families and limited exploration of important areas such as fish fecundity and sustainability. Additional investments in microbial research are needed to ensure the continued expansion and success of freshwater aquaculture.