Third-generation cephalosporin antibiotics induce phage bursts in the human gut microbiome

Additional files to: Third-generation cephalosporin antibiotics induce phage bursts in the human gut microbiome https://doi.org/10.1101/2025.02.07.636470 More information available: https://github.com/EpfeiferNutri/PrediRes Summary: Antibiotics disrupt the gut microbiota, potentially causing long-term health problems and spreading resistance. We studied the impact of a 3-day cephalosporin course on gut phages in 22 healthy individuals, tracking them for six months. Phages, mostly temperate and rarely carrying resistance genes, remained individual-specific despite antibiotic-induced microbiome changes. While phage diversity and abundance decreased by 20% (recovering in 30 to 180 days), a few (mostly virulent) phages bloomed immediately post-treatment, potentially aiding bacterial diversity recovery. Notably, these phages targeted Parabacteroides distasonis, which proliferated only when these phages were absent. Our results highlight phages' crucial role in gut microbiota recovery after antibiotic use.