Antibiotics Carp Skin Microbiome

The skin surfaces of fish harbour diverse assemblages of microbes (microbiomes) that play critical roles in host health and disruption of these microbiomes can lead to disease conditions. Antibiotics, widely used in medicine for human and animal health treatments, are increasingly present in waterways - a growing concern due to their potential to disrupt the balance of microbial ecosystems and drive antimicrobial resistance (AMR). The effects of antibiotics on skin microbiomes in fish, however, have been little explored. Here, we show that a 2-week exposure of Eurasian carp (Cyprinus carpio) to cocktails of five antibiotics (ciprofloxacin, clarithromycin, sulfamethoxazole, trimethoprim, and tetracycline) at levels found in the environment resulted in significant skin bacterial community compositional shifts. Applying 16S rRNA amplicon sequencing, we found enrichment of the genus Arcicella (Proteobacteria) and depletion of Sphaerotilus (Bacteroidetes) with limited recovery even after maintaining the fish for a further two weeks in clean (antibiotic-free) water. In the low-antibiotic concentration exposure group, the tank water microbiome assemblages resembled those of the fish skin suggesting similar responses to the antibiotic treatments. Metagenomic analysis observed no increase in antibiotic resistance genes or changes in metabolic pathway abundance, possibly due to the relatively short duration of antibiotic exposure. This study highlights that even low-level exposure to chemical mixtures can disrupt fish skin microbiome compositions warranting further assessments for long-term effects and functional consequences of these altered microbiomes on fish health.