Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy.
Commun Biol. 2024 Sep 7;7(1):1102. doi: 10.1038/s42003-024-06825-y.
Fusobacteria have been associated to different diseases, including colorectal cancer (CRC), but knowledge of which taxonomic groups contribute to specific conditions is incomplete. We analyzed the genetic diversity and relationships within the Fusobacterium genus. We report recent and ancestral recombination in core genes, indicating that fusobacteria have mosaic genomes and emphasizing that taxonomic demarcation should not rely on single genes/gene regions. Across databases, we found ample evidence of species miss-classification and of undescribed species, which are both expected to complicate disease association. By focusing on a lineage that includes F. periodonticum/pseudoperiodonticum and F. nucleatum, we show that genomes belong to four modern populations, but most known species/subspecies emerged from individual ancestral populations. Of these, the F. periodonticum/pseudoperiodonticum population experienced the lowest drift and displays the highest genetic diversity, in line with the less specialized distribution of these bacteria in oral sites. A highly drifted ancestral population instead contributed genetic ancestry to a new species, which includes genomes classified within the F. nucleatum animalis diversity in a recent CRC study. Thus, evidence herein calls for a re-analysis of F. nucleatum animalis features associated to CRC. More generally, our data inform future molecular profiling approaches to investigate the epidemiology of Fusobacterium-associated diseases.
梭杆菌属与包括结直肠癌（CRC）在内的多种疾病有关，但对于哪些分类群有助于特定疾病的发生，人们的了解并不完整。我们分析了梭杆菌属内的遗传多样性和关系。我们报告了核心基因中的近期和祖先重组，这表明梭杆菌具有镶嵌基因组，并强调分类划分不应依赖于单个基因/基因区域。在各个数据库中，我们发现了大量物种分类错误和未描述物种的证据，这两者都可能使疾病关联复杂化。通过关注包括 F. periodonticum/pseudoperiodonticum 和 F. nucleatum 的谱系，我们表明基因组属于四个现代种群，但大多数已知的物种/亚种都来自于单个祖先种群。在这些种群中，F. periodonticum/pseudoperiodonticum 种群的漂移最小，遗传多样性最高，这与这些细菌在口腔部位的专业化分布较少相符。一个高度漂移的祖先种群则为一个新物种提供了遗传祖先，该新物种包括在最近的 CRC 研究中被归类为 F. nucleatum animalis 多样性的基因组。因此，本文中的证据呼吁重新分析与 CRC 相关的 F. nucleatum animalis 特征。更广泛地说，我们的数据为未来的分子分析方法提供了信息，以研究与梭杆菌相关疾病的流行病学。
