New research in microbial management reveals potential for improvements in fish farming efficiency

The development of effective microbial management strategies to reduce disease outbreaks in aquaculture is often hindered by limited knowledge of the microbiology in fish and shrimp farms.

New research published by the Center for Microbial Ecology and Technology (CMET) at Ghent University (UGent) in Belgium, in collaboration with local research organisation INVE Aquaculture, the Advanced Nutrition business area of Benchmark (BAN) reveals opportunities to drive farming efficiencies through a comprehensive understanding of the microbiome.

“In aquaculture, the presence of bacteria in farming water influences nutrient cycles, metabolic waste degradation, digestion and health of the animals so managing these microbes is an important tool in steering the overall health of the system,” said Peter De Schryver, Group Leader Health and Environment at INVE (BAN) and co-author of the publication.

A good performing microbial community in the water is vital, as well as the need to avoid that the microbiome becomes suddenly disrupted (a process called “dysbiosis”). By accurately assessing the bacteria it allows companies to begin to track changes and link this with the health status of their stock.

In the future this may also allow producers to predict when their animals’ health may be compromised.

First of its kind technology

The researchers focused on the rearing water of white leg shrimp (L. vannamei) cultivation.

They assessed microbiome composition and dynamics using a combination of established molecular and novel flow cytometry analysis methods, which allows to measure and quantify all bacteria, but also algae and sometimes even viruses. This makes it different from conventional diagnostics, which focuses on a single organism at a single moment.

“We tracked contributions of microbes from external sources, including live or dry feed products, to the rearing water,” said publication lead author Jasmine Heyse. “It is the first time that these contributions have ever been quantified.”

Improving efficiency and efficacy of products

“The application of this new flow cytometry methodology means that we can accurately assess changes in microbiomes that are linked to the use of products,” commented Ruben Props, also from UGent. “I believe this opens up new opportunities for product suppliers but also fish and shrimp producers to know that the products they are using are having the desired effect.”

Via CMET’s academic research and upcoming UGent spin-off company Kytos, the researchers are continuing to create larger datasets that will allow them to pinpoint the microbiological markers that determine the survival and health of animals.