Microbiota Imbalance in Salmon Could Be the Cause of Piscirickettsiosis

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By Milthon Lujan

In recent years, scientific research has shed light on the significance of the intestinal microbiome in various species, and fish are no exception. However, the relationships between the environment, diet, microbiome, and fish health are still not well understood.

Currently, the scientific community is questioning whether preventive strategies aimed at exposure to pathogenic species or vaccination alone are sufficient to protect fish health in aquaculture facilities. There is evidence indicating that cooperation among members of bacterial networks may also play a significant role in host defense.


Although it is known that certain pathogenic species are present in the digestive system and intestinal mucosa of healthy fish, the interaction between these bacterial groups and fish health is not fully understood.

A recent article published by researchers from the Pontifical Catholic University of Chile, the Center for Applied Biological Research (CIBA), the University of San Sebastián, the University of Chile, the Technological Metropolitan University, and the Santo Tomás University examines how an imbalanced composition of the intestinal microbiome in fish may be a key factor in promoting bacterial infections.

The researchers aimed to measure the local bacterial communities in the mid-gut digesta and luminal mucosa of Atlantic salmon with and without clinical signs of Salmonid Rickettsial Septicemia (SRS).

Bacterial Collaboration Networks

According to the study, there is a reasonable belief that the colonization of Atlantic salmon (Salmo salar) by bacteria from the pathogenic genus Piscirickettsia has adverse effects on fish development, affecting their size and the timing of harvest.

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The study’s results reveal that pathogenic species such as Aeromonas salmonicida, Renibacterium salmoninarum, Tenacibaculum maritimum, and Piscirickettsia salmonis were detected in the digestive tract and intestinal mucosa of healthy Atlantic salmon, even in the absence of clinical signs of disease. However, the researchers point out that fish exposure to these pathogens may be insufficient to allow colonization and disease.

“Our analysis of metagenomic data indicated that there may be interactions among bacterial members from two or more taxonomic families to create a metabolic phenotype that favors the virulence of P. salmonis,” they reported.

Surprisingly, the frequencies of Piscirickettsia salmonis and other pathogens were higher in fish with Salmonid Rickettsial Septicemia (SRS), but the relative abundance was similar to that observed in healthy fish.

What’s even more intriguing is that fish testing positive for SRS displayed a generalized dysbiosis in the mid-gut and positive growth associations between Piscirickettsiaceae and members of other taxonomic families containing known pathogens.

Metabolic Phenotypes of Bacterial Networks


Furthermore, the reconstruction of metabolic phenotypes based on the bacterial networks detected in the digestive tract and mucosa indicated an over-representation of Gram-negative virulence factors such as colanic acid and O-antigen in SRS-positive fish.

This body of evidence suggests that cooperative interactions between organisms from different taxonomic families within localized bacterial networks may create an environment conducive to P. salmonis causing clinical SRS in the aquaculture environment.

Understanding these intricate relationships between the intestinal microbiome and fish health is crucial in modern aquaculture. This could have significant implications for the prevention and treatment of bacterial diseases in cultivated fish populations. Moreover, it could open new avenues for enhancing fish population health and increasing the sustainability of aquaculture, a vital field in global food production.

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In summary, this study provides a fascinating insight into how the fish’s intestinal microbiota plays a complex role in bacterial infections and fish health. It underscores the need for further research in this area to promote more effective practices in aquaculture and the conservation of fish populations.


Marcos Godoy
Center for Applied Biological Research (CIBA)
1390 Lago Panguipulli Avenue, Puerto Montt, Los Lagos Region, Chile
Email: marcos.godoy@ciba.cl

Reference (Open Access)
Coca, Y., Godoy, M., Pontigo, J.P. et al. Bacterial networks in Atlantic salmon with Piscirickettsiosis. Sci Rep 13, 17321 (2023). https://doi.org/10.1038/s41598-023-43345-x

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