Fig. 5

a-c Longitudinal change of microbiome diversity after antibiotic treatment. Time-dependent change of the microbiome diversity, calculated as the Shannon diversity index based on 16S rRNA reads found by Metaxa2, is shown for the Ampicillin (a), Ciprofloxacin (b), or Fosfomycin (c) cohorts. The diversity index of controls for Ampicillin and Fosfomycin are higher compared to ciprofloxacin. Ampicillin treatment caused a gradual decrease in diversity whereas Fosfomycin treatment caused a steep decline in diversity at 24 h and a small but gradual recovery. Ciprofloxacin treated samples at 24 h were more diverse than control, but the diversity was reduced at 48 and 72 h