The salmon farming industry, while vital for global food security, faces significant challenges in ensuring sustainability. A critical aspect is the health and growth of farmed fish, which are strongly influenced by their diet and gut microbiome. The gut microbiome, a complex community of microorganisms, plays a fundamental role in digestion, nutrient absorption, and overall host health.
Previous research has focused on identifying the types of bacteria present in the gut microbiome of Atlantic salmon (Salmo salar). However, understanding the functional capabilities of these bacteria is essential for developing sustainable aquaculture practices. This knowledge can help optimize feed formulations, improve disease resistance, and reduce environmental impact.
Salmon Microbiome Genome Atlas
To address this knowledge gap, a team of researchers from the Norwegian University of Life Sciences, the University of Galway, the University of Copenhagen, and the Swedish University of Agricultural Sciences has created the Salmon Microbiome Genome Atlas. This comprehensive resource consists of 211 high-quality bacterial genomes, collected from wild and farmed salmon in both freshwater and saltwater environments. These genomes represent a wide range of bacterial species, including 35 distinctive genera and 29 previously undescribed species.
By analyzing the genetic composition of these bacteria, the researchers were able to gain insights into their functional capabilities. Metatranscriptomics, a technique that measures genetic activity, revealed that key bacterial populations in the salmon gut are involved in the breakdown of dietary fibers, the release of essential vitamins, and the production of other beneficial compounds.
Genome-Scale Metabolic Modeling and In Vitro Culturing
To further validate these findings, the researchers conducted in vitro culturing studies and genome-scale metabolic modeling. Metabolic modeling allowed them to predict the metabolic pathways of individual bacterial species, while in vitro culturing enabled them to observe their growth and metabolic activity under controlled conditions.
These experiments confirmed the ability of certain bacteria to break down complex dietary components and produce valuable metabolites. For example, some bacteria were found to degrade plant fibers and release short-chain fatty acids, which have been shown to promote gut health and reduce inflammation. Other bacteria were capable of producing vitamins and other essential nutrients that support salmon growth and development.
“By analyzing the genes of microorganisms, researchers can ‘see’ inside the salmon gut and discover which beneficial bacteria help the fish break down and utilize nutrients from feed,” says Morten Tønsberg Limborg, Associate Professor at the Globe Institute at the University of Copenhagen.
“Thanks to this study, we now understand how the salmon gut microbes function, such as by enhancing nutrient absorption and boosting the immune system. This allows us to develop feeds that tailor the chemical structure of plant-based diet ingredients to the stomach and digestive capabilities of salmon,” says Morten Tønsberg Limborg.
Implications for the Salmon Industry
The Salmon Microbiome Genome Atlas provides a valuable resource for future research on salmon nutrition and health. By understanding the functional capabilities of the salmon gut microbiome, scientists can develop targeted strategies to improve feed efficiency, enhance disease resistance, and reduce the environmental impact of aquaculture.
For example, the information obtained from this study can be used to optimize feed formulations by including ingredients that promote the growth of beneficial gut bacteria. In addition, probiotics and prebiotics can be developed to manipulate the microbiome and promote fish health.
“Salmon aquaculture presents a great opportunity to provide protein-rich, nutrient-dense food. With wild fish populations struggling to meet growing demands, sustainable aquaculture offers a solution to produce more seafood without overfishing,” says Morten Tønsberg Limborg.
He expects that the knowledge gained from research on the salmon microbiome and its ability to digest plant-based feeds could lead to considering these types of feeds for other animals in Danish agriculture, making it more sustainable.
“One of the most exciting discoveries from our study is that some of the beneficial bacteria in salmon can produce essential B vitamins. This is important because we can design future feeds that enhance the growth of these bacterial ‘mini-factories’ that produce essential vitamins instead of adding costly vitamins to the feed,” says Morten Tønsberg Limborg, adding:
“This approach has great potential to improve sustainability for all other animals in our food production systems, such as using insect-based feeds, which are ultra-sustainable.”
Conclusion
In conclusion, the Salmon Microbiome Genome Atlas represents a significant advancement in our understanding of the role of the gut microbiome in sustainable aquaculture. By providing a genomic and functional resource, this study paves the way for the development of innovative approaches to improving the health and well-being of farmed salmon.
Contact
Associate Professor Morten Tønsberg Limborg
+45 61 28 29 84
morten.limborg@sund.ku.dk
Reference
Vera-Ponce de León, A., Hensen, T., Hoetzinger, M. et al. Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health. Nat Microbiol (2024). https://doi.org/10.1038/s41564-024-01830-7
