Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period

This study aimed to characterize the alteration of the fecal microbiome and antimicrobial resistance (AMR) determinants in 24 piglets at day 3 pre-weaning (D. − 3), weaning day (D.0), days 3 (D.3) and 8 post-weaning (D.8), using whole-genome shotgun sequencing. Distinct clusters of microbiomes and AMR determinants were observed at D.8 when Prevotella (20.9%) was the major genus, whereas at D. − 3–D.3, Alistipes (6.9–12.7%) and Bacteroides (5.2–8.5%) were the major genera. Lactobacillus and Escherichia were notably observed at D. − 3 (1.2%) and D. − 3–D.3 (0.2–0.4%), respectively. For AMR, a distinct cluster of AMR determinants was observed at D.8, mainly conferring resistance to macrolide–lincosamide–streptogramin ( mef A), β-lactam ( cfx A6 and aci 1) and phenicol ( rlm N). In contrast, at D. − 3–D.3, a high abundance of determinants with aminoglycoside (AMG) ( sat , aac (6') -aph (2''), aad A and acr F), β-lactam ( fus -1, cep A and mrd A), multidrug resistance (MDR) ( gad W, mdt E , emr A, evg S , tol C and mdt B), phenicol ( cat B4 and cml A4), and sulfonamide patterns ( sul 3) was observed. Canonical correlation analysis (CCA) plot associated Escherichia coli with aac (6') -aph (2''), emr A, mdt B, cat B4 and cml A4 at D. − 3, D.0 and/or D.3 whereas at D.8 associations between Prevotella and mef A, cfx A6 and aci 1 were identified. The weaning age and diet factor played an important role in the microbial community composition.