Monitoring Infection and Antibiotic Treatment in the Skin Microbiota of Farmed European Seabass (Dicentrarchus Labrax) Fingerlings

Abstract The microbiota of fish skin is the primary barrier against disease; however, it is highly dynamic being modulated by several factors. In fish aquaculture, disease outbreaks occur mainly during early-life stages with high associated losses. Antibiotic treatments sometimes remain as the best option to control bacterial diseases, despite many reported negative impacts of its use on fish and associated microbiota. Notwithstanding, studies monitoring the effects of disease and antibiotic treatment on the microbiota of fingerlings are scarce. We used a 16S rRNA metataxonomic approach to assess the impact of a mixed infection with Photobacterium damselae ssp. piscicida and Vibrio harveyi and subsequent antibiotic treatment with flumequine, on the skin microbiota of farmed seabass Dicentrarchus labrax fingerlings. Both disease and antibiotic treatment led to a significant increase in bacterial diversity and core microbial communities and impacted microbial structure. Dysbiosis was confirmed by changes in the abundance of potential pathogenic and opportunistic bacterial taxa. Skin bacterial metabolic function was also significantly affected by flumequine administration, suggesting a detriment to fish skin health. Our results add to an increasing body of literature, showing how fish microbiome response to disease and antibiotics is not easily predicted.