Fig. 1.

Antibiotic impact on the gut microbiome. Trajectories of richness, Shannon diversity, and Simpson’s evenness before treatment (T0) and at the end of the observation period (T3) are shown on phylum rank (a) and species rank (b) for both antibiotic treatments. Pink data points are measurements at T0, purple data points at T3. Boxplots indicate the distribution of data. The connecting magenta line shows the means at each time point and their development under treatment. The p value is displayed at the top of each box and indicates statistical significant differences between T0 and T3 within each treatment cohort (paired t-test). Under ciprofloxacin treatment, richness and Shannon diversity decrease significantly while Simpson’s evenness remains stable. In contrast, under cotrimoxazole, loss of richness and diversity is less pronounced and only significant on the phylum rank. c Violin plots illustrate the differences in baseline values between those patients with a positive baseline-endpoint comparison (BEC, green color) and those with a negative (orange color). The group size is displayed in the respective colors. Baseline species Shannon diversity was higher in the group of patients that lost diversity under cotrimoxazole, while patients with no decline or even an increase in diversity had a lower baseline diversity. The same was observed for species Simpson’s evenness under ciprofloxacin. d Based on multivariate regression modeling, the average percentage change per defined daily dose (DDD) is illustrated for each treatment cohort. Under both antibiotics, a loss in diversity was observed. However, no statistically significant difference was detected between both antibiotics. If an additional impact of concurrent medication was detected beside antibiotics in the multivariate models, this has been illustrated by different filling pattern. e Mean cumulative dose for antimicrobial agents in DDDs for the ciprofloxacin cohort and the cotrimoxazole cohort at each sampling time point (T0–T3). The colors indicate the drug classes, administered in either the ciprofloxacin or cotrimoxazole cohort (illustrated in brackets). The cumulative dose of ciprofloxacin was higher than the dose of cotrimoxazole. f Mean emergence and disappearance of species under antibiotic treatment in percentage compared to the species count at baseline. Frequent potentially pathogenic species are displayed. The number of patients with an emergence or disappearance of these species is shown in brackets