Towards informed antimicrobial use in aquaculture: How fish age, species and climate shape gut microbiome responses to florfenicol and peracetic acid

Introduction

Antibiotics and antiparasitics are essential for managing infectious diseases in commercial aquaculture, particularly in high-density rearing systems like hatcheries. While antibiotics have been linked to increased abundance of antibiotic resistance genes and persistent shifts in the intestinal microbiome of farmed fish, the influence of underlying host factors (age, species), environmental determinants (climate) and co-application with antiparasitics on microbiome dynamics remains unclear.

Goals

This study focused on the effects of antimicrobial treatment on the gut microbiome of brown trout (Salmo trutta) and nile tilapia (Oreochromis niloticus), exploring the co-selective pressure of combined florfenicol (FF) and peracetic acid (PAA) on microbial composition and how host age, climate, and species shape the microbiome"s response to antimicrobial exposure.

Methods

In a freshwater recirculating system (9 – 11 °C), adult and juvenile brown trout were subjected to three treatments (10 mg/kg bw FF, FF+PAA, 0.005% PAA) compared to an untreated control group. Adult nile tilapia in a pond system (24 – 28 °C) received 10 mg/kg bw FF. Fecal samples were collected before treatment, on the last day of treatment (day 10) and four times during the post-treatment phase, followed by 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform.

Results

Fish age and species significantly shaped the gut microbiome response to FF and PAA treatment, with juvenile trout showing greater microbiome volatility than adults. Changes included declines in beneficial commensals (Cetobacterium, Lactococcus), whose network positions remained altered despite recovered abundance by day 28. FF impacts were enhanced in warmer climates, with shifts persisting up to day 30 and reduced bacterial diversity in tilapia. Aeromonas, Streptococcus and Cetobacterium were identified as common responders following FF treatment.

Summary

Addressing a critical knowledge gap regarding the extent to which the response to antimicrobials is dependent on the developmental stage of the fish and rearing climate, our study emphasizes the importance of integrating gut microbiome characteristics related to fish age and species in aquaculture management practices. This study also provides the first evidence that external PAA application disrupts gut microbial communities, highlighting potential long-term consequences of combined use of antibiotics and antiparasitics.