Fusobacterium nucleatum (Fn), a bacterium present in the human oral cavity and rarely found in the lower gastrointestinal tract of healthy individuals¹, is enriched in human colorectal cancer (CRC) tumours^2,3,4,5. High intratumoural Fn loads are associated with recurrence, metastases and poorer patient prognosis^5,6,7,8. Here, to delineate Fn genetic factors facilitating tumour colonization, we generated closed genomes for 135 Fn strains; 80 oral strains from individuals without cancer and 55 unique cancer strains cultured from tumours from 51 patients with CRC. Pangenomic analyses identified 483 CRC-enriched genetic factors. Tumour-isolated strains predominantly belong to Fn subspecies animalis (Fna). However, genomic analyses reveal that Fna, considered a single subspecies, is instead composed of two distinct clades (Fna C1 and Fna C2). Of these, only Fna C2 dominates the CRC tumour niche. Inter-Fna analyses identified 195 Fna C2-associated genetic factors consistent with increased metabolic potential and colonization of the gastrointestinal tract. In support of this, Fna C2-treated mice had an increased number of intestinal adenomas and altered metabolites. Microbiome analysis of human tumour tissue from 116 patients with CRC demonstrated Fna C2 enrichment. Comparison of 62 paired specimens showed that only Fna C2 is tumour enriched compared to normal adjacent tissue. This was further supported by metagenomic analysis of stool samples from 627 patients with CRC and 619 healthy individuals. Collectively, our results identify the Fna clade bifurcation, show that specifically Fna C2 drives the reported Fn enrichment in human CRC and reveal the genetic underpinnings of pathoadaptation of Fna C2 to the CRC niche.

具核梭杆菌( Fn ) 是一种存在于人类口腔中的细菌，很少在健康个体的下胃肠道中发现¹，但在人类结直肠癌 (CRC) 肿瘤中含量丰富^2,3,4,5。高肿瘤内Fn负载与复发、转移和较差的患者预后相关^5,6,7,8。在这里，为了描述促进肿瘤定植的Fn遗传因素，我们生成了 135 个Fn菌株的封闭基因组；来自非癌症个体的 80 种口腔菌株和从 51 名 CRC 患者的肿瘤中培养的 55 种独特癌症菌株。泛基因组分析确定了 483 个富含 CRC 的遗传因子。肿瘤分离菌株主要属于Fn动物亚种( Fna )。然而，基因组分析表明，Fna被认为是单一亚种，但却由两个不同的进化枝（Fna C1 和Fna C2）组成。其中，只有Fna C2 在 CRC 肿瘤生态位中占主导地位。 Inter- Fna分析确定了 195 个Fna C2 相关遗传因素，这些因素与代谢潜力增加和胃肠道定植一致。为了支持这一点，Fna C2 治疗的小鼠肠道腺瘤数量增加，代谢物发生改变。对 116 名 CRC 患者的人类肿瘤组织进行微生物组分析，结果显示Fna C2 富集。 62 个配对样本的比较表明，与正常邻近组织相比，只有Fna C2 是肿瘤富集的。对 627 名 CRC 患者和 619 名健康个体粪便样本的宏基因组分析进一步支持了这一点。总的来说，我们的结果确定了Fna进化枝分叉，表明Fna C2 特别驱动了人类 CRC 中报道的Fn富集，并揭示了Fna C2 对 CRC 生态位的病理适应的遗传基础。