Introduction

Amid the growing demand for sustainable protein-rich nutrition, particularly in regions disproportionally affected by the ongoing food crisis, aquaculture has become a pivotal resource. Antibiotics and Antiparasitics, extensively used in hatcheries to maximize production yields and as surrogates for inadequate hygiene, have been linked to increased abundance of antibiotic resistance genes and persistent shifts in the intestinal microbiome of various farmed fish species. Given that the gut microbiome of juvenile fish is still maturing, it likely exhibits greater susceptibility to external perturbations compared to the more stable microbiome of adult fish.

Goals

Using a metabarcoding approach, this study focuses on the distinct impact of antimicrobial treatment on the gut microbiome of juvenile and adult brown trouts (Salmo trutta fario), exploring the co-selective pressure of combined florfenicol (FF) and peracetic acid (PAA) application as well as the influence of age.

Material & Methods

In a freshwater RAS, one and two summer-old brown trouts underwent three treatments (10 mg/kg FF via medicated feed, FF+PAA, PAA) compared to an untreated control group. Fecal samples were collected prior to administration, on the last day of administration (day 10) and four times during the post-treatment phase, followed by 16S rRNA gene based amplicon sequencing on the Illumina MiSeq platform.

Results

Results show distinct changes in the gut microbiome composition of juvenile trout following both FF and PAA treatment, marked by decreased abundance of several beneficial core taxa (Shewanella, Lactococcus, Deefgea) and an increase of putative pathogens (Streptococcus, Acinetobacter). Notably, these effects were absent in adult fish.

Summary

Addressing a critical knowledge gap regarding the extent to which the response to antimicrobial treatment is dependent on the developmental stage of the fish, this study emphasizes the importance of understanding differential effects between developmental stages and highlights the potential long-term consequences of combined application of antibiotics and antiparasitics in aquaculture.