New doctoral thesis on the microbial composition of the gut in salmonids
Shuowen Cao has studied how biological, environmental, and, above all, dietary factors affect the gut microbiota of salmonids, with a particular focus on rainbow trout (Oncorhynchus mykiss).
Dissertation December 18
Fish farming, or aquaculture, has become the fastest-growing food production sector in the world. As demand for seafood continues to rise, aquaculture plays an increasingly important role in ensuring that future generations have access to nutritious and sustainable sources of protein. However, this growth brings new challenges. To remain sustainable, aquaculture must find alternatives to traditional feed ingredients such as fishmeal and soy, which are expensive, environmentally demanding, and compete with food resources for humans and livestock.
A major key to overcoming these challenges may lie within the fish themselves — specifically, in the complex community of microorganisms that inhabit their intestines, known as the gut microbiota. These microbial populations are not just passive passengers; they actively influence digestion, nutrient absorption, metabolism, immune defence, and even behaviour. In other words, a healthy gut microbiota contributes to healthy, resilient fish. Understanding how different factors, especially diet, affect this internal ecosystem can help scientists design feeds that support both fish welfare and environmental sustainability.
This thesis investigated how biological, environmental, and dietary factors shape the gut microbiota of salmonid fish, focusing primarily on rainbow trout (Oncorhynchus mykiss), one of the most widely farmed freshwater species. It also explored the potential of microbial-based feed ingredients, such as fungi and yeasts, as innovative alternatives to conventional protein sources.
The first part of the research took a big-picture approach by combining data from many previously published studies on the gut microbiota of Atlantic salmon and rainbow trout. This meta-analysis revealed that the composition of gut microbes in salmonids is strongly affected not only by diet and environment but also by differences in experimental methods, such as how samples are collected and how DNA sequencing is performed. These findings highlight a crucial point: to compare results across studies and build reliable knowledge, the aquaculture research community needs more standardized approaches for sampling, sequencing, and data analysis.
The second study explored a novel use for filamentous fungi, microorganisms that can be cultivated on industrial by-products. Four fungal species (Aspergillus oryzae, Neurospora intermedia, Rhizopus delemar, and 118 Rhizopus oryzae) were grown on ethanol-production stillage, a leftover material from biofuel production, and then tested as potential protein sources in rainbow trout diets. Although these fungal ingredients were slightly less digestible than the standard control feed, they had a notable impact on the gut microbiota, increasing microbial diversity and potentially contributing to gut health. This suggests that with further optimization to improve digestibility, fungal biomass could become a valuable and sustainable feed ingredient that also helps recycle industrial waste streams.
In the third study, the focus shifted to probiotics, live microorganisms that can provide health benefits to the host. Two yeast species, Kluyveromyces marxianus and Rhodosporidium babjevae, were tested as dietary supplements in rainbow trout. The results showed that R. babjevae in particular promoted beneficial bacterial groups in the intestine and influenced the expression of immune-related genes. These effects suggest that this yeast could strengthen the fish’s natural defences and improve overall health, offering a promising addition to future aquaculture feeds.
Together, the findings from these studies deepen our understanding of how fish feed composition interacts with the intestinal microbiota and fish physiology. They demonstrate that microbial-based ingredients, whether in the form of fungi used as feed proteins or yeasts used as probiotics, can contribute to more sustainable, health-promoting aquaculture systems.
By harnessing the power of beneficial microbes and repurposing waste materials into valuable feed components, this research supports a shift toward circular and environmentally responsible aquaculture. Ultimately, it brings us one step closer to feeding the world’s growing population without compromising the health of our ecosystems or the fish that sustain them.
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