The microbiota of salmon is transplanted into sea bream to understand the impact of diet

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By Milthon Lujan

Schematic representation of the intestinal microbiota transplant (IMT) from Atlantic salmon (Salmo salar) to gilthead seabream (Sparus aurata) and subsequent nutritional assay carried out for assessing the effect of the diet in the gut bacterial communities. Source: Ruiz, et al., (2024); Sci Rep.
Schematic representation of the intestinal microbiota transplant (IMT) from Atlantic salmon (Salmo salar) to gilthead seabream (Sparus aurata) and subsequent nutritional assay carried out for assessing the effect of the diet in the gut bacterial communities. Source: Ruiz, et al., (2024); Sci Rep.

Imagine if we could improve the health and performance of fish by changing their microbial populations. That’s exactly what researchers are exploring with “intestinal microbiota transplants” (IMT).

A team of researchers from IRTA conducted an intestinal microbiota transplant (TIM) between two species of marine carnivorous fish that thrive in different environmental conditions: from the donor Atlantic salmon (Salmo salar) to the recipient sea bream (Sparus aurata), after destroying their baseline microbiota with antibiotic treatment.

The study examined the possibility of transplanting intestinal microbes from one fish species to another, delving into the intricate relationship between intestinal microbes and their hosts, and exploring how they impact health and potential strategies to promote a healthy microbiome.

The power of partnership

For millions of years, fish, like other animals, have co-evolved with their intestinal microbes, forming a mutually beneficial partnership known as the “holobiont.” These small residents not only reside passively; they play crucial roles in:

  • Digestion and nutrient absorption: Breaking down food, extracting vital nutrients, and converting them into energy.
  • Modulation of the immune system: Training and regulating the immune system to fight pathogens and maintain balance.
  • Barrier function and mucosal integrity: Protecting against harmful invaders and ensuring intestinal health.

Scientists have been exploring the salmon microbiome, including the European Union project AquaIMPACT, which supports this growth by researching the intestinal microbiota of various fish species.

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Factors shaping our microbiome

According to scientific literature, several elements influence our intestinal microbiota, including:

  • Host-specific and non-specific factors: Age, genetics, immune system function, and even sleep patterns.
  • Environmental conditions: Diet, physical activity, antibiotic use, and exposure to contaminants.
  • Species-specific characteristics: Each animal species, including fish, harbors a unique intestinal microbiome adapted to its specific needs and environment.

Microbiome modulation

Research teams in different parts of the world are exploring various strategies to promote a healthy intestinal microbiome, including:

  • Diet: Consumption of prebiotics (food for beneficial bacteria) and probiotics (live beneficial bacteria) may favor a healthy intestinal environment.
  • Fecal microbiota transplant (FMT): Transfer of healthy gut bacteria from a donor to improve the recipient’s health.
  • Intestinal microbiota transplant (IMT): Similar to FMT but specifically targeting the entire intestinal microbial community in smaller animals such as fish.

The potential of IMTs in fish

Recent studies using IMT in fish species such as salmon and sea bream show promising results, suggesting their potential to:

  • Improve growth and reproductive performance
  • Enhance digestive capacity and intestinal health
  • Increase resilience to environmental stressors
  • Enhance intestinal microbial diversity

When things go wrong

The intestinal microbiota plays a crucial role in digestion, immunity, and overall health. But what happens when this delicate balance is disrupted?

An imbalance in the intestinal microbiota, known as dysbiosis, is linked to various diseases, including digestive disorders, metabolic imbalances, inflammatory conditions, and even neurological disorders. Understanding the factors influencing this delicate ecosystem is crucial for maintaining health.

Inter-species microbe transplantation

The study used Atlantic salmon as the donor and sea bream as the recipient. Both are carnivorous fish but thrive in different environments. Researchers first “cleaned” the recipient’s intestinal microbiome with antibiotics and then transplanted microbes from the donor.

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Subsequently, scientists tested different strategies to see how the recipient’s intestinal microbiota responded:

  • Fasting versus diet: One group of recipients received no food, while others received their typical diet or a diet similar to that of the donor.
  • Tracking microbes: Over time, researchers analyzed the recipient’s intestinal bacteria to see how different conditions affected their composition.

Results: a microbiome remix

The sea bream’s intestinal microbiome recovered, but it wasn’t just a copy of the salmon’s. It was unique, influenced by the donor, the recipient, and… the diet! Thus, sea bream fed their usual diet developed a “typical” microbiome, while those fed the salmon’s diet developed a unique “fusion” microbiome, incorporating elements from both species and the food.

The study revealed some fascinating findings:

  • A fresh start is key: Clearing the existing microbiome with antibiotics was crucial for the transplanted microbes to establish themselves.
  • Diet shapes the community: Fish fed their typical diet reverted to their original composition of intestinal bacteria.
  • The salmon’s diet creates a fusion: Fish fed the donor’s diet developed a unique “fusion” microbiome, incorporating elements from both species and the food.

What does this mean for fish health?

These results suggest that IMTs have the potential to improve fish health, but several key factors need to be considered:

  • Targeted intestinal cleansing: Complete removal of the existing microbiome may be necessary for successful transplantation.
  • Diet plays a crucial role: Tailoring the diet to the desired microbiome composition is essential for long-term benefits.
  • Species compatibility matters: Further research is needed to understand how the microbiomes of different species interact.

The future of fish microbiome management

The intestinal microbiome is a dynamic ecosystem that adapts to both donor microbes and recipient diet. Thus, this research opens the doors to personalized microbiome management in fish, adapting treatments and diets to specific needs and environmental conditions.

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By optimizing fish intestinal health, we could improve their growth, disease resistance, and overall well-being. While more research is needed, IMTs could become a powerful tool for sustainable and responsible aquaculture practices.


Understanding fish intestinal microbiota is a powerful tool for promoting health and well-being. By exploring innovative strategies like TIM, we can unlock the potential of a healthy microbiome for a healthier future for all living beings.

By optimizing the intestinal microbiota, we can improve fish growth, survival, and disease resistance, ultimately leading to healthier fish and a more sustainable aquaculture industry.

The study has been funded through the ADIPOQUIZ project, financed by the Ministry of Science, Innovation, and Universities of Spain.

Alberto Ruiz.
Aquaculture Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de La Ràpita, Crta. Poble Nou, km 5.5, 43540, La Ràpita, Spain
Email: alberto.ruiz@irta.cat

Reference (open access)
Ruiz, A., Gisbert, E. & Andree, K.B. Impact of the diet in the gut microbiota after an inter-species microbial transplantation in fish. Sci Rep 14, 4007 (2024). https://doi.org/10.1038/s41598-024-54519-6