摘要：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 (
mefA), β-lactam (
cfxA6 and
aci1) and phenicol (
rlmN). In contrast, at D. − 3–D.3, a high abundance of determinants with aminoglycoside (AMG) (
sat,
aac(6')
-aph(2''),
aadA and
acrF), β-lactam (
fus-1,
cepA and
mrdA), multidrug resistance (MDR) (
gadW,
mdtE
, emrA,
evgS
, tolC and
mdtB), phenicol (
catB4 and
cmlA4), and sulfonamide patterns (
sul3) was observed. Canonical correlation analysis (CCA) plot associated
Escherichia coli with
aac(6')
-aph(2''),
emrA,
mdtB,
catB4 and
cmlA4 at D. − 3, D.0 and/or D.3 whereas at D.8 associations between
Prevotella and
mefA,
cfxA6 and
aci1 were identified. The weaning age and diet factor played an important role in the microbial community composition.
