Greater difference between wild salmon and farmed salmon than researchers thought

Salmon ends up on dinner plates all over the world. Yet few people think about what goes on inside the fish, more specifically in its gut, where a community of bacteria quietly goes about its business.

What actually goes on in the digestive tract of salmon?

Researchers have now investigated how the thousands of different organisms living in the fish gut develop in salmon from Norway, Scotland and Ireland.

Important for Norwegian industry

Farmed salmon is one of Norway's most important exports. A better understanding of the microbes that live in fish could help reduce disease. It could also improve fish health and lay the foundation for more sustainable production.

The researchers behind the study have analysed a total of 847 samples of gut contents from Atlantic salmon (Salmo salar). They also examined samples of feed and the water in which the fish lived.

The analysed fish came from both freshwater and seawater. The sample included both farmed and wild salmon that have different diets and grow in different environments.

Farmed salmon has lower bacterial diversity

The results reveal a clear difference between wild and farmed salmon. The difference is greater than many of the researchers had expected.

“We saw that in farmed salmon, the diversity of bacteria is lower, and the composition is also different than in wild salmon. By comparison, we found that the bacteria in farmed salmon are more specialised and adapted to life in cages,” says Wasimuddin, a researcher at the Norwegian Veterinary Institute.

This may sound effective, but it can also be a disadvantage, he explains:

“In nature, variety is often a strength. A rich diversity of bacteria is often associated with a robust immune system and greater resilience against diseases. When diversity shrinks, fish can become more vulnerable to diseases.”

Loses diversity as it grows

The study shows that bacterial diversity in the gut decreases as the salmon grows. Some types of bacteria gradually disappear. Others become more dominant.

This is consistent with what researchers call ecological succession, which means that the community in microorganisms gradually changes over time.

Some species become less common or disappear. Others increase and become dominant. The community of organisms is increasingly shaped by the host and its diet.

This same pattern has been reported in earlier studies.

The analyses point to one type of dominating bacteria in particular: Mycoplasma. It is found in greater quantities in salmon and seems to take space from other bacteria.

“It's a genus of bacteria that has evolved alongside salmon for thousands of years, essentially becoming a dominant gut bacteria,” says Wasimuddin.

The researchers do not yet know what this means in practice. This is one of the major knowledge gaps identified by the study. But the researchers suspect that such changes could affect both the health and growth of the fish.

Type of feed can affect fish health

The researchers identify what the salmon eats as the most important factor. The study demonstrated that around 23 per cent of the variation in the bacterial composition of farmed salmon can be explained by diet alone.

Farmed salmon are given standardised feed, while wild salmon eat a varied diet in the wild. This results in different bacterial communities.

Because the gut microbiome has been linked to disease resistance and stress response in fish more broadly, the finding that diet has such a strong influence on gut bacteria raises the possibility that feed choices could indirectly affect how robust farmed salmon are.

The study also points to how the environment around the fish plays a role. The effect varies from region to region and throughout its life cycle.

“This is important knowledge for the aquaculture industry. The bacteria in the gut are not just passengers. They influence how robust the individual is against disease and stress,” Wasimuddin explains.

Could make farming more sustainable

The findings point to something very central: Farming practices can be improved by taking intestinal bacteria into account.

The right feed and a better environment could result in healthier fish and more sustainable production. Establishing the right microbiome is therefore not just a scientific curiosity. It is also an economic necessity.

At the same time, the researchers issue a clear warning.

It is important to preserve the rich bacterial diversity found in wild salmon. This diversity may be crucial when the fish face new challenges in a changing environment.

Protecting wild salmon populations is therefore not just about conservation. It is also a way of preserving their unique microbial diversity. This is a biological resource whose value for fish health and resilience we are only beginning to understand.

Could become a new 'health check' tool

The study also provides an important tool for the future. Monitoring the gut microbiome is increasingly being explored as a way to gauge animal health. Changes in the bacterial community could provide early indications of problems before other symptoms appear.

The researchers have created a kind of baseline showing what the gut microbiota of wild salmon looks like across different geographical areas.

Wasimuddin explains that such a tool could be used to track environmental impacts, detect stress and disease in fish, and monitor the health of wild salmon populations. The concept could also be applied to other fish species.

In short, monitoring the bacteria in the gut can act as an early warning system.

What happens next?

The researchers emphasise that the work needs to continue. Knowing which bacteria are present is only the first step.

“Now we want to go deeper and find out how the different bacteria in the gut, and also those residing on the skin and gills, actually work within the fish's body,” says Wasimuddin.

They want to answer the following questions:

• How do the bacteria affect the immune system?

• How do they interact with each other?

• How do they influence fish health overall?

By combining new methods that map the function of the bacteria, and not just what they are, the researchers hope to find answers.

"If the industry puts this knowledge of the salmon gut to use, it could generate positive ripple effects far beyond the confines of the fish cage," says Wasimuddin.

References:

Heys et al. Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar, Applied and Environmental Microbiology, 2020. DOI: 10.1128/aem.02283-19

Wasimuddin et al. Ecological dynamics of the Atlantic salmon gut microbiota across developmental phases and geographic regions, Communications Biology, 2026. DOI: 10.1038/s42003-026-10264-2

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