The large-scale farming of Atlantic salmon (Salmo salar) faces a constant threat: infectious diseases, which not only compromise fish welfare but also significantly increase production costs. Understanding how salmon internally defend themselves against different pathogens is crucial for developing more effective management strategies.
Although numerous studies on the salmon’s response to individual diseases exist, a comprehensive analysis directly comparing these responses was lacking. A new study by researchers from Gyeongsang National University has filled this gap through a comparative multi-transcriptomic analysis, using public data to reveal the unique gene expression patterns in Atlantic salmon facing four of the sector’s most relevant pathogens: the bacterium Piscirickettsia salmonis, the viruses PMOV and ISAV, and the parasite causing amoebic gill disease (AGD).
The results, published in the scientific journal Developmental & Comparative Immunology, offer an unprecedented and holistic view of the complex host-pathogen interactions, showing that each disease leaves a distinctive genetic “signature” on the fish.
Key conclusions
- Each pathogen (P. salmonis, PMOV, ISAV, and AGD) triggers a unique and distinct transcriptomic “signature” in the head kidney of Atlantic salmon.
- Infection by Piscirickettsia salmonis is characterized by the activation of cell signaling pathways and the remodeling of the actin cytoskeleton, a structure the bacterium appears to manipulate.
- Amoebic gill disease (AGD) causes a notable activation of metabolic pathways in the head kidney, even more so than general immune responses.
- Despite belonging to the same viral family, PMOV and ISAV induce opposite responses: PMOV strongly activates defenses, whereas ISAV suppresses most biological processes.
How was the salmon’s response studied?
To achieve a robust comparison, the researchers conducted a meta-analysis of 82 Atlantic salmon head kidney transcriptomes, obtained from previously published studies. The head kidney was chosen as it is a key organ in modulating immune and stress responses in fish.
The key to this work was the application of an identical bioinformatics pipeline to process all the data. This eliminated variations that could arise from using different analytical methods, allowing for a direct and reliable comparison of how the salmon’s genes are “turned on” or “turned off” (i.e., their expression) during each of the four distinct infections.
A genetic “signature” for each disease
The first fundamental finding was that, despite originating from different experiments, the transcriptomic profiles consistently grouped according to the type of pathogen causing the infection. This confirms that the salmon’s response is highly specific to each threat.
Of the thousands of genes whose expression changed, only 11 were common to all four diseases, underscoring the specificity of the response. In contrast, between 37% and 73% of the affected genes in each infection group were exclusive to that particular pathogen, forming a true “genetic signature” of the disease.
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The salmon’s unique responses to each pathogen
The detailed analysis revealed the biological strategies that salmon deploy against each infectious agent.
Piscirickettsia salmonis: Remodeling cellular defenses
Infection with the intracellular bacterium P. salmonis showed a unique pattern: a strong activation of pathways related to the regulation of the actin cytoskeleton and associated cell signaling pathways (such as Rap1 and PI3K-Akt). The cytoskeleton is the cell’s internal scaffolding, and the bacterium appears to manipulate it for its own benefit, forcing the host to respond by activating the genes for these components.
Interestingly, the bacterial infection also caused a marked suppression of the ribosome pathway, the cellular machinery responsible for producing proteins. This could be a host strategy to limit pathogen replication or a consequence of bacterial toxins.
AGD: A metabolism-centered response
Amoebic gill disease (AGD), caused by an ectoparasite that does not directly infect the head kidney, generated a surprising systemic response. Instead of a predominant immune activation, the AGD infection was characterized by a strong and significant activation of numerous metabolic pathways.
Scientists observed an upregulation of pathways related to amino acid metabolism (arginine, proline, glutathione, etc.) and lipid metabolism (fatty acid degradation). This suggests that the head kidney may play a crucial role in the systemic immune response through metabolic activation, possibly to supply energy or defensive molecules to affected tissues like the gills.
PMOV vs. ISAV: Two viruses, two opposing strategies
Although both viruses belong to the same family (Orthomyxoviridae), the responses they elicited in the salmon were drastically different, almost opposite.
- Infection by PMOV triggered a robust response, activating key pathways such as the proteasome and protein processing in the endoplasmic reticulum. This is typical of cells needing to increase protein and energy production to fight an active viral infection.
- Infection by ISAV, in contrast, was characterized by a widespread suppression of most biological processes. Instead of activating defenses, the transcriptome of ISAV-infected fish showed a downward trend in gene expression. This could indicate that ISAV is more stealthy or that the host’s response is fundamentally different, which aligns with the different pathological manifestations of both viruses.
Conclusion: Implications for the future of salmon farming
This comparative study provides a more comprehensive perspective than analyses of individual pathogens. By establishing the specific “transcriptomic signatures” for P. salmonis, PMOV, ISAV, and AGD, this research provides a valuable map of the biological responses of Atlantic salmon.
Understanding these differences is fundamental. For instance, knowing that P. salmonis targets the cytoskeleton or that AGD triggers a massive metabolic response opens new avenues for developing targeted therapies, functional diets, or genetic selection programs that strengthen the most relevant defense pathways for each disease. These findings not only deepen our knowledge of fish immunology but also lay the groundwork for more precise and effective health management in salmon aquaculture.
Contact
HyeongJin Roh
Department of Aquatic Life Medicine, College of Marine Sciences, Gyeongsang National University
Tongyeong, 53064, Republic of Korea
Email: hjroh@gnu.ac.kr
Reference
Kang, G., & Roh, H. (2025). Comparative multi-transcriptomic analysis of Atlantic salmon (Salmo salar) under distinct pathogen infections. Developmental & Comparative Immunology, 170, 105452. https://doi.org/10.1016/j.dci.2025.105452
Editor at the digital magazine AquaHoy. He holds a degree in Aquaculture Biology from the National University of Santa (UNS) and a Master’s degree in Science and Innovation Management from the Polytechnic University of Valencia, with postgraduate diplomas in Business Innovation and Innovation Management. He possesses extensive experience in the aquaculture and fisheries sector, having led the Fisheries Innovation Unit of the National Program for Innovation in Fisheries and Aquaculture (PNIPA). He has served as a senior consultant in technology watch, an innovation project formulator and advisor, and a lecturer at UNS. He is a member of the Peruvian College of Biologists and was recognized by the World Aquaculture Society (WAS) in 2016 for his contribution to aquaculture.
