Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas

Researchers administered the antibiotic cefotaxime to three surgically treated giant pandas and tracked changes in their gut microbiome and resistome over time using 16S rRNA sequencing and shotgun metagenomics. They found that antibiotic treatment caused a sharp shift in bacterial community composition (notably a rise in Pseudomonadota and drop in Bacillota), and reduced microbial diversity; these changes began to reverse somewhat during recovery. At the same time, the overall diversity of antibiotic-resistance genes (ARGs) and virulence factor genes (VFGs) remained largely unchanged — but a specific class (the CTX-M β-lactamase family) increased and stayed elevated even post-treatment. Nature The study suggests that while short-term antibiotic use significantly perturbs gut microbial communities in giant pandas, it may not dramatically expand the resistome broadly — though it does selectively enrich some resistance genes.