Multi-omics surveillance of antimicrobial resistance in the pig gut microbiome

High-throughput sequencing technologies are increasingly used to monitor global health challenges, such as antimicrobial resistance. A study using shotgun metagenomics and metatranscriptomics analyzed the effect of different treatments on the transcriptome and resistome of pig gut microbiome in post-weaning diarrhea. A metagenome-assembled genome (MAG) catalogue was generated from 140 pig fecal samples. Results showed that antimicrobial resistance genes (ARGs) were significantly reduced at the assembly level, and half of those ARGs were detected transcriptionally active in all treatment groups. Differential gene expression showed differential expressed genes (DEGs) against the amoxicillin-treated group, correlated with antimicrobial resistance.