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. 2022 May 21;16(9):2065–2075. doi: 10.1038/s41396-022-01252-5

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — The impacts of antibiotics (n = 11, Amo = amoxicillin, Azi = azithromycin, Aztr = aztreonam, Cip = ciprofloxacin, Col = colistin, Doxy = doxycycline, Lev = levofloxacin, Merp = meropenem, Met = metronidazole, SulTri = bactrim and Tob = tobramycin) compared to untreated control samples on (A) Shannon index ratio, (B) Weighted UniFrac distance, (C) pathogen to fermenter log ratio, and (D) rRNA gene copy ratio. Individual points are colored by patient (n = 24). The shaded areas behind the boxplots are regions of the plot where the outcomes of our theoretical predictions and/or model iteration 1 would lie if correct, colored according to antibiotic treatment type (T_w, T_p, and T_f). Kruskal-Wallis statistics are reported in Table S8. Asterisks denote p-value significance where ****p ≥ 0.0001, ***p ≥ 0.001, **p ≥ 0.01, *p ≥ 0.05. Mann-Whitney post hoc tests are reported in the Supplementary material (Tables S10–S16).