Impact of Florfenicol on the Intestinal Microbiome and Salmon Health

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By Milthon Lujan

The use of antibiotics in aquaculture is a common practice to prevent and treat diseases in fish. However, concerns have been raised worldwide regarding the impact of antibiotics on aquatic organisms and their surrounding ecosystems. Antibiotics are often used therapeutically to treat existing diseases in fish, but their misuse can have detrimental effects on fish health.

Recent studies have shown that antibiotic treatments can lead to dysbiosis in the fish gut microbiome, resulting in decreased growth and increased vulnerability to infections. Despite the attention given to the impacts of antibiotics on aquatic organisms, little is known about how these medications affect the intestinal microbial communities of fish and their overall health.

A study conducted by scientists from the University of Stavanger, the University of Florida, the U.S. Geological Survey, the University of California, and Skretting Aquaculture Innovation focused on investigating the effects of florfenicol (FFC) on the intestinal microbiome and gastrointestinal gene expression in juvenile Atlantic salmon (Salmo salar).


In this study, scientists used post-smolt Atlantic salmon raised in tanks with continuous water flow at a temperature of 12°C and a 24-hour photoperiod with oxygen levels above 90% saturation. Three different doses of florfenicol (FFC) were administered in the experimental diet of the salmon: 10, 20, and 30 mg/kg of fish body weight. The diet was provided for 18 days, followed by a 10-day recovery period.

Assessing the complex interactions between the gut microbiome and the host requires the use of advanced sequencing techniques. In this regard, scientists employed a transcriptomic and metatranscriptomic approach to analyze the fish’s gut microbiome and gene expression. Metatranscriptomics allows for a better understanding of interactions between the gut microbiome and the fish, as well as the development of innovative strategies to improve fish health and enhance aquaculture industry efficiency.


The results revealed that doses of 10 and 30 mg/kg of FFC led to downregulation of genes involved in the transcription of NADH-ubiquinone oxidoreductase chain-1, suggesting that the antibiotic affects bacterial respiratory metabolism. The 30 mg/kg FFC dose increased the expression of genes encoding glycolytic enzymes, such as phosphoglycerate kinase, indicating an alteration in energy metabolism within the microbiome.

Moreover, the fish’s transcriptome analysis showed that FFC treatment affected cellular processes in the fish’s gastrointestinal system, including pathways related to apoptosis and DNA metabolism. In particular, the highest FFC dose activated pathways associated with cellular regulation, such as LXR/RXR activation, FXR/RXR activation, and protein ubiquitination. At the end of the recovery period, the group treated with 30 mg/kg of FFC altered pathways related to EIF2 signaling and lysine degradation.


The fish’s gut microbiome plays a vital role in metabolism and energy balance, influencing nutrient absorption and hormone release. Certain bacteria have been reported to protect the host from diseases through nutrient competition and the production of antimicrobial compounds. The study identified molecular-level effects of FFC treatment on the intestinal microbiome and the gastrointestinal system of juvenile Atlantic salmon. Importantly, despite these molecular-level changes, no phenotypic alterations in fish growth or condition were observed.

According to the study’s findings, most of the observed changes were reversible and diminished at the end of the recovery period, with the exception of the high-dose treatment group.


“While no significant effects on fish growth were observed, metatranscriptome results demonstrated that an 18-day treatment with 10 and 20 mg/kg bw of florfenicol had various effects on the gut microbiota gene expression,” concluded the scientists.

This study underscores the importance of understanding the molecular mechanisms underlying the effects of antibiotics in the salmon industry. Although the observed molecular effects may not necessarily translate into noticeable changes in fish health, these findings emphasize the need to optimize antibiotic treatments in aquaculture, thereby minimizing potential environmental impacts and promoting more sustainable practices in the industry.

Understanding the effects of antibiotics on the gut microbiome and fish health is essential for making informed and responsible decisions in aquaculture production.

Giovanna Monticelli
Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger
Stavanger, Norway

Daniela M. Pampanin
Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger
Stavanger, Norway

Giovanna Monticelli, Joseph H. Bisesi, Jason T. Magnuson, Daniel Schlenk, Carlos Zarza, David Peggs, Daniela M. Pampanin. Effect of florfenicol administered through feed on Atlantic salmon (Salmo salar) gut and its microbiome, Aquaculture, 2023, 740310, ISSN 0044-8486, https://doi.org/10.1016/j.aquaculture.2023.740310.

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