Mapping the metagenomic landscape: combined shotgun sequencing and quantitative PCR to profile gut metagenome-assembled genomes in marmosets following treatment with a broad-spectrum antibiotic cocktail.

Broad-spectrum antibiotics are invaluable tools for treating pathogenic infections, but their sustained use can contribute to changes in gut microbiome membership and the emergence of antimicrobial resistance. While these unintended side effects are independently well documented, the relationship between them has seldom been investigated. To address this, we quantified the effects of 28-d antibiotic cocktail exposure on metagenome-assembled genomes and antibiotic resistance genes in common marmosets using a custom whole-genome shotgun sequencing pipeline and quantitative polymerase chain reaction assays. We observed contrasting genus-level reductions in Bifidobacterium abundance and Fusobacterium growth, both during antibiotic treatment and a 2-week post-treatment period. Total bacterial abundance was not significantly affected by antibiotics, likely due to the presence of antibiotic-resistant opportunists. Genes for vancomycin resistance and multidrug efflux pumps were identified in metagenome-assembled genomes of an unclassified Sarcina sp. and Escherichia coli, respectively, and were accompanied by increased abundance of these species during treatment. Additionally, we detected 11 dysregulated metagenomic pathways related to carbohydrate metabolism, including 2 pathways relevant to short-chain fatty acid production, following antibiotic exposure. This study provides insights into the species-dependent emergence of antimicrobial resistance mechanisms in non-human primates following antibiotic exposure that could be relevant for antibiotic therapies and resistance management.