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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.

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