The effect of oxytetracycline treatment on the gut microbiome community dynamics in rainbow trout (Oncorhynchus mykiss) over time

Antibiotic compounds play an important role in the control of bacteria disease outbreaks on fish farms. Yet, the impact of commercially licensed antibiotics on the diversity and composition of the gut microbiome in some farmed fish species remains unclear. The following study explored the effect of a low-level oxytetracycline treatment on the gut microbiome community in rainbow trout (Oncorhynchus mykiss) (average weight 152.8 ± 8.9 g). In this study, fish were fed diets with or without oxytetracycline (35 mg/kg bodyweight/day) for 7-days, followed by a 14-day withdrawal period. Distal gut digesta samples were collected from individual fish in a time series manner (on days 0, 2, 8, 10, 15 and 22). The microbiome community was profiled from the gut digesta using next generation sequencing of the bacterial 16S rRNA gene. No mortality was observed and all animals remained clinically healthy throughout the study. Furthermore, results showed that oxytetracycline treatment led to significant changes in the gut microbiome of rainbow trout. Oxytetracycline treatment led to a decline in Mycoplasma and Bacillus in treated fish compared with control fish, accompanied by an increase in Aeromonas, Deefgea and Pseudomonas. The gut microbiome of treated fish continued to change after antibiotic treatment and was not found to stabilise by the end of the study. After 14-days withdrawal from the antibiotic, treated fish displayed microbiomes with significantly higher microbial richness compared with control fish. Moreover, a number of taxa were found to become enriched in the distal guts of treated fish by day 22 including Aeromonas, Brevinema and Deefgea as well as diet-associated Chloroplast_ge. However, this was accompanied by a decline in the prevalence of Bacillus and Clostridium_sensu_stricto_1. Further work is required to better understand the long-term impacts of antibiotics and post-antibiotic recovered gut microbiome communities on the health and welfare of fish.