Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change

The gut microbiome is implicated in the pathogenesis of colorectal cancer (CRC), but the full scope of this dialogue is unknown. Here we aimed to define the scale and membership of the body of CRC- and health-associated gut bacteria in global populations. We performed a microbiome-CRC correlation analysis of published ultra-deep shotgun metagenomic sequencing data from global microbiome surveys, utilizing a de novo (reference-agnostic) gene-level clustering approach to identify protein-coding co-abundant gene (CAGs) clusters. We link an unprecedented approximately 23-40 percent of gut bacteria to CRC or health, split nearly evenly as CRC- or health-associated. These microbes encode 2,319 CAGs encompassing 427,261 bacterial genes significantly enriched or depleted in CRC. We identified many microbes that had not previously been linked to CRC, thus expanding the scope of known unknowns of CRC-associated microbes. We performed an agnostic CAG-based screen of bacterial isolates and validated predicted effects of previously unimplicated bacteria in preclinical models, in which we observed differential induction of precancerous adenomas and field effects. Single-cell RNA sequencing disclosed microbiome-induced senescence-associated gene expression signatures in discrete colonic populations including fibroblasts. In organoid co-cultures, primary colon fibroblasts from mice with microbiomes promoted significantly greater growth than fibroblasts from microbiome-depleted mice. These results offer proof-of-principle for gene-level metagenomic analysis enabling discovery of microbiome links to health and demonstrate that the microbiome can drive precancer states, thereby potentially revealing novel cancer prevention opportunities.

肠道微生物组（gut microbiome）与结直肠癌（colorectal cancer, CRC）的发病机制密切相关，但二者间互作的完整范围仍未明确。本研究旨在明确全球人群中与结直肠癌及健康状态相关的肠道细菌的组成规模与成员构成。我们对全球微生物组调研已发表的超深度鸟枪法宏基因组测序数据开展了微生物组-结直肠癌关联分析，采用从头（不依赖参考基因组，reference-agnostic）的基因水平聚类策略，识别编码蛋白质的共丰度基因簇（co-abundant gene clusters, CAGs）。我们首次将约23%~40%的肠道细菌与结直肠癌或健康状态建立了明确关联，其中与结直肠癌相关和与健康相关的细菌占比几乎均分。这些微生物共编码2319个共丰度基因簇，涵盖427261个细菌基因，这些基因在结直肠癌样本中呈现显著的丰度上调或下调。我们发现了多种此前未被报道与结直肠癌相关的微生物，由此拓展了结直肠癌相关微生物的已知未知领域的边界。我们采用无偏的基于共丰度基因簇的筛选方法对细菌分离株进行了筛查，并在临床前模型中验证了此前未被关联的细菌的预测效应，观察到癌前腺瘤与癌场效应（field effects）的差异化诱导现象。单细胞RNA测序（single-cell RNA sequencing）结果显示，在包括成纤维细胞在内的离散结肠细胞群中，存在微生物组诱导的衰老相关基因表达特征。在类器官共培养体系中，携带完整肠道微生物组的小鼠原代结肠成纤维细胞的增殖能力显著强于微生物组缺失（无菌）小鼠的成纤维细胞。本研究结果为基因水平宏基因组分析提供了概念验证，该分析方法可用于发现微生物组与健康状态的关联，并证实肠道微生物组可推动癌前状态的发生，由此有望为癌症预防提供全新的干预思路与潜在靶点。