Exploring Gut Microbiota Composition and Occurrence of Selected Antimicrobial Resistance Genes in Domestic Pigs and Urban and Sylvatic Wild Boars from Sicily

This exploratory study compared gut microbiota composition and targeted detection of eight antimicrobial resistance genes (ARGs) among three geographically and ecologically distinct Sicilian populations: domestic pigs (DP), urban wild boars (WB-U), and sylvatic wild boars (WB-S). Ileal samples were collected from 36 animals (12 per group) and profiled by 16S rRNA gene (V3-V4) sequencing and PCR screening for β-lactam (blaTEM, blaCTX-M IV, blaOXA, blaSHV) and tetracycline (tetA, tetB, tetC, tetD). Firmicutes and Proteobacteria dominated all groups. DP showed high abundance of Psychrobacter and Pseudomonas, whereas Lactobacillus prevailed in WB-U; WB-S showed an intermediate profile. Community composition differed among groups (PERMANOVA, p = 0.001). Pairwise comparisons identified differences between DP and each WB group (p = 0.0015 for both), but not between WB-U and WB-S (p = 0.302). blaTEM detection frequencies were 83.3% in WB-U, 16.7% in WB-S, and 50.0% in DP, with a significant WB-U–WB-S difference (p = 0.0099). tetA was detected in 41.7% of DP and 33.3% of WB-U; tetC only in WB-U (25.0%). These findings provide baseline information of differences in gut microbiota composition and in the detection of selected ARGs, while informing future surveillance strategies at the wildlife–livestock–human interface.