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<p>The genus <i>Fusobacterium</i> encompasses significant pathogens implicated in diseases spanning from infections to cancer. However, taxonomic ambiguities persist within the genus, particularly concerning <i>Fusobacterium nucleatum</i> (<i>sensu lato</i>). Through genus-wide average nucleotide identity (ANI) and phylogenetic analyses of 540 <i>Fusobacterium</i> genomes, we identify an ANI gap (93.38%−93.89%) for species delineation, leading to comprehensive taxonomic revisions that resolve these ambiguities. We further establish <i>gyrB</i> and <i>rpoB</i> as high-resolution taxonomic markers with phylogenies consistently supporting the revised taxonomy. Leveraging these markers, we develop B&amp;B, a general strategy for precise species identification without whole-genome sequencing, and validate its accuracy in clinically relevant strains. Integrating the revised taxonomy with genomic/metagenomic toolkits demonstrate broad utilities, reinterpreting key colorectal cancer-associated species. This work establishes a unified taxonomic framework and enables standardised species classification for <i>Fusobacterium</i> isolates and microbiomes, highlighting the genetic divergence among <i>Fusobacterium</i> species and providing the taxonomic precision essential for advancing <i>Fusobacterium</i>-related research.</p>

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Integrating ANI and phylogenies for re-evaluation of Fusobacterium taxonomy and disease associations

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年3月10日

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  • Dexi Bi,
  • Yuli Wu,
  • Guo Ji,
  • Xingchen Zhu,
  • Hao Li,
  • Ruting Xie,
  • Yaohui Gao,
  • Zixin Deng,
  • Dongyan Han,
  • Huanlong Qin,
  • Qing Wei

摘要

The genus Fusobacterium encompasses significant pathogens implicated in diseases spanning from infections to cancer. However, taxonomic ambiguities persist within the genus, particularly concerning Fusobacterium nucleatum (sensu lato). Through genus-wide average nucleotide identity (ANI) and phylogenetic analyses of 540 Fusobacterium genomes, we identify an ANI gap (93.38%−93.89%) for species delineation, leading to comprehensive taxonomic revisions that resolve these ambiguities. We further establish gyrB and rpoB as high-resolution taxonomic markers with phylogenies consistently supporting the revised taxonomy. Leveraging these markers, we develop B&B, a general strategy for precise species identification without whole-genome sequencing, and validate its accuracy in clinically relevant strains. Integrating the revised taxonomy with genomic/metagenomic toolkits demonstrate broad utilities, reinterpreting key colorectal cancer-associated species. This work establishes a unified taxonomic framework and enables standardised species classification for Fusobacterium isolates and microbiomes, highlighting the genetic divergence among Fusobacterium species and providing the taxonomic precision essential for advancing Fusobacterium-related research.