Fig. 1. Fn niche features.

a, A schematic of Fusobacterium strain collection (n = 146) and the sequencing strategy for unique strains. SMRT, single-molecule real-time sequencing. b, A column graph depicting the proportion of Fusobacterium genomes, subset by species, within the CRC (orange) and oral (blue) niches. The inset shows all non-Fn species of Fusobacterium (Fnec, F. necrophorum; Fu, F. ulcerans; Fp, F. pseudoperiodonticum; Fc, F. canifelinum; Fv, F. varium). c, The composition of the Fn pangenome subset by niche. Anvi’o²¹ gene cluster (GC) prevalence was used to define core (≥95%), accessory (≥5% and <95%) and rare (<5%) features conserved in both CRC-associated and oral-associated strains (collection core, ≥95% in all strains within the collection; collection cloud, ≥5% and <95% in all strains within the collection; collection rare, <5% in all strains within the collection). Disparate features are those that do not fall into any of the other noted bins. d, The proportion of niche-enriched gene clusters across CRC-associated and oral-associated Fn genomes. The plot box shows the 25th percentile, median and 75th percentile. The plot whiskers indicate the minima and maxima. e, KofamKOALA KEGG orthologue analysis²⁷ of niche-enriched gene clusters. f, A column graph depicting the proportion of Fn genomes, grouped by subspecies, within the CRC and oral niche. Statistical analysis was carried out using a two-sample z-test, two-tailed. NS, not significant. g, Gene presence–absence heat map of canonical Fn virulence factors (fadA (refs. ^38,39,42), fap2 (ref. ³⁴), fplA (ref. ³³), radD (refs. ^36,62), aim1 (ref. ³⁵), cmpA (ref. ³⁷) and fusolisin³²) across Fn subspecies, in which each column represents an individual genome (Fna n = 75, Fnn n = 17, Fnp n = 33, Fnv n = 10). The heat map is organized using an rpoB gene-based phylogenetic tree. For each genome, the tree end points indicate the niche origin (CRC (orange); oral (blue)) and the bar colour indicates the Fn subspecies (Fna (red); Fnn (gold); Fnp (purple); Fnv (brown)). The graphics in a were created using BioRender.com.