Researchers create first ever resource of Atlantic salmon-derived bacterial genomes

To make salmon farming more sustainable and the salmon healthier, we need to replace seafood-based salmon feed with other types of feed. But how do gut bacteria help the salmon digest the feed and absorb nutrients? Can the salmon become a vegetarian? Researchers are now aiming to find out.

Salmon are natural carnivores. When living wild in nature, they eat insects, insect larvae, small herring, crustaceans, and animal plankton.

Researchers and feed producers are now exploring plant-based alternatives to reduce reliance on fishmeal and fish oil. This involves developing feeds made from ingredients like algae, soy, peas, and even insects, aiming to give salmon the nutrients they need without relying on marine resources.

"But before we start using these new types of feed, we need to better understand what is happening inside the salmon's gut, in order to optimize the impact on the fish's nutrition and health," says Sabina Leanti La Rosa.

She is an Associate Professor at the Norwegian University of Life Sciences (NMBU) and has recently co-led a study on how salmon bacteria interact and digest feed, published in the renowned journal Nature Microbiology.

Good bacteria in the salmon gut

Together with research colleagues at NMBU and several international collaborators, she has analyzed the genetic material of as many as 211 different microorganisms that they have found in the gut of Atlantic salmon.

"This is the first overview that has been made of bacterial genetic material from Atlantic salmon. The material is collected through traditional cultivation methods in the laboratory and advanced DNA sequencing methods using samples from both wild and farmed fish in fresh and salt water," says La Rosa.

The analyses of the genes of the microorganisms allow the researchers to "see" into the salmon's gut and reveal which "good" bacteria help the fish to break down and utilize the nutrients in the feed, and which molecular mechanisms they use for this.

"We have also identified some particularly important bacteria in the salmon's gut, which are capable of producing and releasing vitamins and other substances known to promote growth, health and well-being," she says.

The Protein Engineering and Proteomics Group ( PEP )
PEP-gruppen Bildet viser Sabina Leanti La Rosa
Forsker , Fakultet for biovitenskap
Institutt for husdyr- og akvakulturvitenskap — Sabina Leanti La Rosa, Associate Professor at the Norwegian University of Life Sciences (NMBU). Photo: Håkon Sparre

Understanding the gut

"Thanks to this new study, we can now understand how the microbes in the salmon gut function. This allows us to develop nutritional strategies that adapt the chemical structure of the new feed ingredients we want to add to the salmon diet, to the enzymatic tools that the gut microbiota have to break them down," says Professor Phil Pope.

He is a co-lead of this study and one of the project leaders for ImprovAFish, which this research is part of.

The Protein Engineering and Proteomics Group ( PEP )
PEP-gruppen Bildet viser Phillip Pope
Førsteamanuensis
Fakultet for biovitenskap
Institutt for husdyr- og akvakulturvitenskap — Professor Phil Pope. Foto: Håkon Sparre

Can the salmon digest plant-based feed?

"There is a need to improve the sustainability of fish feed, and salmon aquaculture is trying to turn salmon, a carnivorous fish, into a “vegetarian”," says Sabina Leanti La Rosa.

"As the demand for food continues to rise alongside the growing world population, salmon aquaculture presents a huge opportunity to provide high-protein, nutrient-rich food. With wild fish stocks struggling to meet the increasing needs," sustainable aquaculture offers a solution to produce more seafood without overfishing, she says.

To be able to switch to plant-based feed, or to use health-promoting prebiotic additives in the salmon diet, it is crucial to understand how the gut microbiota can help the fish digest and utilize the new nutrients.

The salmon itself has very few enzymes in the gut to break down and utilize plant-based food and prebiotics. In the Nature Microbiology study, the researchers wanted to learn more about how the microorganisms in the salmon gut function.

"By studying the specific microbial populations in the salmon gastrointestinal tract, we can identify which bacteria promote better digestion of plant materials and boost the fish's immune system, making the fish more resilient to diseases and infections.

"If we understand how the salmon gut microbiota work, we can design strategies to enhance the fish's ability to grow and thrive on novel and more sustainable diets, eventually contributing to producing bigger and healthier fish for human nutrition," says Arturo Vera Ponce de Leon. He is a researcher at NMBU and the first author of the study in Nature Microbiology.

bildet viser Arturo Vera Ponce De Leon Postdoktor
Fakultet for kjemi, bioteknologi og matvitenskap , NMBU — NMBU-forsker Arturo Vera Ponce de Leon. Foto: Håkon Sparre

Hoping for healthier salmon

The researchers hope that the aquaculture industry will utilize their results and develop more resource-efficient feed formulations and supplements (like prebiotics) tailored to the digestive capabilities of salmon and the salmon gut microbiota, leading to improved growth rates, health, and overall fish welfare.

"Eventually this will help to enhance the nutritional quality of farmed salmon, ensuring that consumers receive fish that is not only healthier but also richer in beneficial nutrients," says La Rosa.

She hopes that more researchers will make use of the overview of the genetic material they have created, which is named SMGA.

"SMGA is a powerful resource for forthcoming studies where scientists can look deeper into the complex interactions between diet, gut microbiota, and fish metabolism. We really encourage future studies to further expand the overview of the salmon gut microbiota.

"Indeed, the study of salmon gut microbiota is still in its early stages compared to the more extensive research conducted on the gut microbiota of humans and other production animals. By leveraging the lessons learned from other species, this knowledge can lead to innovations in aquaculture practices and the development of new, more effective feeds for improved fish health, sustainability, and nutrition in aquaculture systems."

about the research:

Salmon Gut Microbiome

The article Genomic and Functional Characterization of the Atlantic Salmon Gut Microbiome in Relation to Nutrition and Health was published in Nature Microbiology Monday October 14, 2024.
NMBU-researchers involved in the study: Arturo Vera Ponce de Leon, Sabina Leanti La Rosa, Phil Pope, Simen R. Sandve, Torgeir R. Hvidsten
Research groups: Microbial Ecology and Meta-omics group (MEMO), Protein Engineering and Proteomics Group (PEP), CIGENE, BIAS group
Norwegian partners: Christian René Karlsenved NOFIMA
International partners:

Prof Ines Thiele, Dr Tim Hensen and Dr Bronson Weston at the University of Galway, Galway, Ireland
Prof Stefan Bertilsson and Dr Matthias Hoetzinger at Swedish University of Agricultural Sciences, Uppsala, Sweden
Associate Prof. Morten T. Limborg and lab members at the University of Copenhagen, Copenhagen, Denmark