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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. 5 — (A) Model iteration 2 outcomes of 16S rRNA gene copy ratio of each patients’ actual sputum Pathogen/Fermenter ratio was used as input to the model (n = 24). Individual points are colored by antibiotic treatment (n = 11). The dotted grey line denotes no change from treatment. Subsequent experimental validation using two communities, P1 and P2 (n = 10), showing the (B) pH in relation to log rRNA gene copies, (C) Approximate pH, (D) Pathogen/Fermenter log ratio, (E) log rRNA gene copies, (F) Genera abundance, (G) Distribution based on genera-classification as classical pathogen or anaerobic fermenter. Asterisks denote p-value significance where ****p ≥ 0.0001, ***p ≥ 0.001, **p ≥ 0.01, *p ≥ 0.05.