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. 2025 Aug 23;13:189. doi: 10.1186/s40168-025-02178-8

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© The Author(s) 2025

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. 3 — Differential gene expression (DGE) analysis in response to bacterial presence in Crohn’s disease. A DGE analysis in all cells. The top panel shows the rate of significant DGE in response to various bacteria. The heatmap below displays Z-scores of DGE for various bacterial species. B Gene set enrichment analysis (GSEA) of upregulated genes in all cells in response to bacterial presence. C GSEA of downregulated genes in all cells in response to bacterial presence. D DGE analysis in immune cell-rich areas. E DGE analysis in enterocyte-rich areas. F GSEA of upregulated genes in immune cell-rich areas in response to bacterial presence. G GSEA of upregulated genes in enterocyte-rich areas in response to bacterial presence