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. 2024 Feb 16;30(3):785–796. doi: 10.1038/s41591-024-02803-3

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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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Fig. 1 — a, For each microbial SGB listed, slopes are shown (that is, whether it is increasing or decreasing over study visits) in patients with PFS ≥12 (n = 83) and PFS <12 months (n = 92), respectively. For increased readability, SGBs differentially abundant in only one study visit have been removed (see Extended Data Fig. 2 for all SGBs). Red and blue colors indicate whether the focal SGB is increasing or decreasing in its abundance over study visits, respectively, with the strength of the colors corresponding to the steepness of the slope, with darker shades indicating steeper increases/decreases. It then shows, in the teal–brown heatmap, the average difference between the two slopes (that is, between patients with PFS ≥12 and PFS <12 months) across the different study visits. Non-gray cells in the heatmap correspond to the focal SGB’s log fold change in abundance between patients with PFS ≥12 and PFS <12 months, respectively. Teal cells correspond to study visits for which the abundance of the focal SGB is higher in patients with PFS ≥12 than with PFS <12 months, and vice versa for brown cells (at 90% BCL). Gray cells denote differences between patients with PFS ≥12 and PFS <12 months whose 90% credible interval cover zero. b, Three example features and how they increase and/or decrease in their expected abundance (represented in centered log ratio coordinates) over the study visits in patients with PFS ≥12 months (yellow slope) and in patients with PFS <12 months (purple slope). For each microbial SGB or pathway, the inset figure then displays the average difference between the two slopes at each study visit, including its 90% credible interval. These averages are the same as depicted in the teal–brown heatmap in a, and significance is deemed by evaluating whether or not the 90% credible interval covers zero. c, Microbial pathways are shown, similar to the format in a. The number (n) represents the number of patient samples at each visit for patients with PFS ≥12 and PFS <12 months.