Emerging diseases and the roles of microbiomes in tilapia farming

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By Milthon Lujan

Researchers from the University of Exeter and WorldFish have published a scientific review on tilapia production, highlighting the issues associated with diseases and treatments. They also examine the importance of microbiomes for fish health.

Diseases and treatments

Tilapia is considered a very disease-resistant fish; however, the intensification of tilapia farming is showing that tilapia succumbs to several disease-causing organisms.

Tilapia is particularly susceptible to infection by Streptococcus sp. including Streptococcus dysgalactiae, S. iniae, and S. agalactiae, which are now among the most important bacterial pathogens, causing significant economic losses worldwide.

Outbreaks of streptococcosis can be treated with antibiotics if administered in the early stage of the disease, but oral administration can be challenging as infected fish lose their appetite.

Currently, several vaccines are available for the treatment of streptococcosis, including AQUAVAC® Strep Sa (Merck Animal Health Company, USA), AquavacTM GarvetilTM (Intervet/Schering-Plough Animal Health), and NORVAX® STREP Si (Merck Animal Health Company, USA).

Other key emerging bacterial pathogens include Francisella noatunensis subsp. orientalis causing francisellosis, Flavobacterium columnare causing columnaris, Aeromonas hydrophila, A. jandaei, and A. veronii causing motile aeromonad septicemia (MAS), Vibrio spp. causing vibriosis, and edwardsiellosis caused by Edwardsiella ictaluri and E. tarda. Other facultative opportunistic fungal infections include Saprolegnia spp. and protozoa, including Ichthyophthirius multifiliis, Trichodina spp., and Dactylogyrus spp.

To date, eight viral diseases (five DNA viruses and three RNA viruses) have been reported in tilapia, some of which cause significant losses in tilapia aquaculture.

Viral diseases such as herpes-like virus, iridoviral disease (IVD), viral nervous necrosis (VNN), tilapia lake virus (TiLV), and infectious spleen and kidney necrosis virus (ISKNV) affecting Nile tilapia and red hybrid tilapia are the most limiting viral disease agents in tilapia farming.

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Microbiomes of tilapia’s superficial mucosa

The skin and gills of fish represent the main routes for pathogens to invade fish and act as a critical line of defense to maintain host health.

The epithelial surfaces of fish skin and gills are covered with a layer of mucus containing various immunogenic compounds, including antimicrobial compounds and enzymes, proteins such as immunoglobulins, defensins, lysozymes, proteases, esterases, and mucins.

Although mucosal surfaces can represent a hostile environment, adapted microbes can resist the immunological components that abound on these surfaces. In turn, these commensals act as an additional line of immunological defense to obstruct pathogen colonization through antagonistic activity and to compete for adhesion sites and/or nutrients.

Disrupting the symbiotic host-microbiome relationship can lead to significant changes in the microbiota community structure in a process called “dysbiosis.”

Stressful conditions, which often occur in aquaculture practices, can cause changes in the microbiota to favor the spread of opportunistic pathogens, which are naturally present in the aquatic environment and/or part of the fish microbiome.

Factors that influence the mucosal microbiome

Diseases are often context-dependent, and pathogens can be present in the biomes (water, sediment, biofilms) of the culture environment. Moving to a disease state depends on many biotic and abiotic factors that influence the diversity and composition of the fish skin microbiome, as these factors contribute to the inherent variability of microbiome composition among individuals.

Water quality

The external surface of fish is continuously exposed to water, resulting in a dynamic relationship between the planktonic and microbial communities on the skin surface. Since the pond planktonic communities may be influenced by water quality, it is not surprising that water quality also has a significant impact on the bacterial communities of fish skin.

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Geographic location and habitat

Geographic location has been reported as one of the strongest predictors of fish skin microbial communities; however, much of this is likely related to different environmental parameters, which can influence planktonic communities. Each geographic location probably has a multitude of environmental factors and habitat characteristics that influence the fish skin microbiome processes.


Specific host factors also govern fish microbial assemblages. These are particularly important for the gastrointestinal microbiome, while environmental factors have greater relevance for the skin mucosal surface.

Undoubtedly, fish skin microbiomes show a high degree of variation among individuals, even among fish of the same species in the same environment.


Under stress-free conditions, the balance of microbiomes in fish works to help prevent pathogens from entering and causing diseases. Genetics also play a complementary role, highlighting the breadth and complexity of the environmental and host-associated processes that govern fish microbiome composition.

Effects of antibiotics on fish microbiomes

The uncontrolled use of antibiotics in aquaculture can spread antimicrobial resistance, which has not been well studied. In addition, the misuse of antibiotics can have immediate implications for the microbiomes associated with aquaculture, as antibiotics can attack the commensal bacteria that support fish health, immune function, and disease resistance.

In this regard, antibiotics can reduce the mass and/or diversity of the microbial community, and/or change enzymatic functions.


According to the study authors, urgent research and support are needed to combat emerging diseases, and this requires a more fundamental understanding of the prevalence, spread, and pathogenesis of the disease to support the development of specific treatments and vaccines.

They also highlight that the adoption of effective management and biosafety plans, including increased training for fish farmers on disease management and the misuse of antimicrobials, is required.

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Finally, “a deeper understanding of the mucosal microbiomes associated with health and disease should allow for the development and application of more effective probiotics for fish aquaculture,” the researchers conclude.

Sanjit Chandra Debnath
Faculty of Health and Life Sciences
University of Exeter
Exeter, EX4 4QD, Devon, UK

Charles R. Tyler
Faculty of Health and Life Sciences
University of Exeter
Exeter, EX4 4QD, Devon, UK

Reference (open access)
Debnath, S.C., McMurtrie, J., Temperton, B. et al. Tilapia aquaculture, emerging diseases, and the roles of the skin microbiomes in health and disease. Aquacult Int (2023). https://doi.org/10.1007/s10499-023-01117-4

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