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. 2024 Mar 20;628(8007):424–432. doi: 10.1038/s41586-024-07182-w

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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. 3 — a, A gene presence versus absence column graph depicting the proportion of Fna genomes containing canonical Fn virulence factors, subset by clade (Fna C1 (green); Fna C2 (lavender)). The statistical analysis was carried out using a two-sample z-test, two-tailed. b, Left: computational confocal analysis of colon cancer epithelial cells (HCT116; grey) co-incubated with representative Fna C1 (green) or Fna C2 (lavender) strains. Scale bars, 4 μm. Right: a bar plot demonstrating the percentage of HCT116 cells with intracellular Fna; n = 3 biological replicates with 3 analysed z-stacks. Data are plotted as mean ± s.e.m. The statistical analysis was carried out using Welch’s t-test, two-tailed. c, A PPanGGOLiN⁵¹ map of the Fna pangenome. Each node represents a gene group, syntenic nodes represent neighbouring genes, the size indicates relative presence across Fna genomes, and the colour depicts pangenome partition (Fna core (red); Fna C1 accessory genome (green); Fna C2 accessory genome (lavender)). The white arrows (left panel) and oblongs (right panel) indicate Fna C2-associated putative eut and pdu operons. d, Schematics of these Fna C2 operons. An interactive PPanGGOLiN map is available at https://fredhutch.github.io/fusopangea/. e,f, Differentially expressed genes (log₂[fold change] ≥ 0.58 and ≤−0.58 with −log₁₀[P value] ≥ 1.30) in a representative Fna C2 strain, SB010, exposed to EA (e) or 1,2-PD (f) compared to unexposed SB010 control. To highlight SB010-unique content, genes also differentially expressed under the same exposure conditions in a representative Fna C1 strain, KCOM 3764, have been removed (Extended Data Fig. 4b,c). The vertical dotted lines indicate the threshold of significant gene expression, defined as log₂[fold change] ≥ 0.58 and ≤−0.58. The statistical analysis was carried out using glmQLFTest, two-sided. The data point colours indicate Fna core (red), Fna C1 accessory (green), Fna C2 accessory (lavender) or Fna cloud (black; present in ≥5% and <95% in all Fna strains) genes. The stars indicate eut and pdu operon genes.