Abstract The rise in antibiotic resistance is an emerging global problem that affects not only humans but also livestock. This increase in antimicrobial resistance may partly be due to the overuse or misuse of antibiotics in livestock. Growing evidence indicates that antibiotic use in livestock influences the emergence of antibiotic-resistant pathogens. To test the impact of antibiotic use on the gut microbial ecology in pigs, we evaluated the impact of two currently used antibiotics (carbadox/copper sulfate (AB1) and chlortetracycline/tiamulin hydrogen formate (AB2)) in nursery pigs. To this end, a 56-day feeding trial was conducted using 192 pigs with an average body weight (BW) of (3.1 ± 0.73 kg) in two replicates (96 pigs per rep). The pigs were assigned to one of three dietary treatments (CON: No antibiotics, AB1: Carbadox/copper sulfate, AB2: Chlortetracycline/tiamulin) with 4 pens per treatment and 8 pigs per pen in a randomized complete block design in each replicate. Fecal samples were collected on day 28 of birth before administration of treatments and on the last day of nursery stage (day 56) after antibiotics for microbiome analysis. The bacterial community composition of the fecal samples was assessed by sequencing the V4 region of the 16S rRNA gene. The AB1 and AB2 groups demonstrated a significantly greater number of bacterial taxa (amplicon sequence variants (ASVs)) compared to the no antibiotic treatment for both reps. Beta -diversity identified distinctive clustering between baseline and treated groups (AB1 and AB2) and revealed significant differences in bacterial community composition when CON vs AB1 or AB2 were compared (p 0.05). Differential abundance analysis identified several significant ASVs in the treated groups (AB1 and AB2), including members of the genera Lactobacillus, Faecalibacterium, Segatella, and Akkermansia. Additionally, microbial community profiling indicated that the genus Lactobacillus and phylum Bacillota varied between treated and untreated pigs. Overall, these findings provide important insights into the immediate impacts of antibiotic exposure on the porcine gut bacteriome, and future work will focus on assessing long-term effects through a longitudinal study investigating AMR gene abundance and AMR gene -taxa relationships in the gut microbiome to develop microbiome-based intervention strategies to mitigate antibiotic use.
Munezero et al. (Wed,) studied this question.