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Fig. 3. | BMC Biology

Fig. 3.

From: Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study

Fig. 3.

Antibiotic impact on the gut plasmidome. a Trajectories of total plasmid abundance, plasmid abundance from proteobacteria, plasmid Shannon diversity, and plasmid Simpson’s evenness before treatment (T0) and at the end of the observation period (T3) are shown 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). Total plasmid abundance, plasmid abundance from Proteobacteria, and plasmid diversity decreased significantly under ciprofloxacin treatment while plasmid evenness remained stable. In contrast, plasmids were not strongly affected by cotrimoxazole. b Based on multivariate regression modeling, the average percentage change of plasmid characteristics per defined daily dose (DDD) is illustrated for each treatment cohort. Bonferroni-corrected statistically significant differences between both antibiotics (LR p < 0.002) are presented by single asterisks. If an additional impact of concurrent medication was detected beside antibiotics in the multivariate models, this has been illustrated by a different filling pattern (checkerboard pattern = virostatic agents, horizontal stripes = antifungal agents, vertical stripes = virostatic and antifungal agents). Trends for plasmid evenness were significantly different, with a slight increase under ciprofloxacin and moderate decrease under cotrimoxazole. c, d The co-occurrence network displays the relationship between ARG-carrying plasmids from certain taxonomic origins and the ARG classes located on these plasmids at each sample collection time point for the ciprofloxacin cohort (c) and the cotrimoxazole cohort (d). The total plasmid-ARG content is expressed by the line width between plasmid origin and ARG class. The bar on the upper right part of each network row displays the scale of the total plasmid-ARG content (range 1–27). The diagrams in the lower right parts illustrate the Proteobacteria plasmid-ARG content for aminoglycoside, sulfonamide, trimethoprim ARGs, and beta-lactamase A enzymes. The y-axis ranges from 1 to 27 and displays the respective plasmid-ARG content. The ARG classes in the diagrams correspond to the colors of the networks and the legend at the bottom of the graph. Plasmids harboring ARGs from Proteobacteria expanded under cotrimoxazole, while ARG-containing plasmids from all origins declined under ciprofloxacin

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