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. 2024 Feb 19;14:4068. doi: 10.1038/s41598-024-53506-1

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Strain replacement analysis. The Figure visualizes strain dynamics for combinations of bacterial species and sampling timepoints for which sufficient Illumina short-read data was available. Each species is represented by a main panel; main panels are labeled with patient IDs on the y-axis and sampling times on the x-axis. Each dot represents one sampling event, and each horizontal line represents the period between two sampling events. Horizontal lines are colored according to whether a strain replacement event was determined to have taken place between the two sampling events (orange) enclosing the line. Additional symbols indicate adverse events.