Butyrivibrio   and   Pseudobutyrivibrio   dominate in anaerobic gastrointestinal microbiomes, particularly the rumen, where they play a key role in harvesting dietary energy. Within these genera, five rumen species have been classified (  Butyrivibrio fibrisolvens  ,   Butyrivibrio hungatei  ,   Butyrivibrio proteoclasticus  ,   Pseudobutyrivibrio ruminis   and   Pseudobutyrivibrio xylanivorans  ) and more recently an additional   Butyrivibrio   sp. group was added. Given the recent increase in available genomes, we re-investigated the phylogenetic systematics and evolution of   Butyrivibrio   and   Pseudobutyrivibrio  . Across 71 genomes, we show using 16S rDNA and 40 gene marker phylogenetic trees that the current six species designations (  P. ruminis  ,   P. xylanivorans  ,   B. fibrisolvens  ,   Butyrivibrio   sp.,   B. hungatei   and B. proteclasticus) are found. However, pangenome analysis showed vast genomic variation and a high abundance of accessory genes (91.50–99.34 %), compared with core genes (0.66–8.50 %), within these six taxonomic groups, suggesting incorrectly assigned taxonomy. Subsequent pangenome accessory genomes under varying core gene cut-offs (%) and average nucleotide identity (ANI) analysis suggest the existence of 42 species within 32 genera. Pangenome analysis of those that still group within   B. fibrisolvens  ,   B. hungatei   and   P. ruminis  , based on revised ANI phylogeny, also showed possession of very open genomes, illustrating the diversity that exists even within these groups. All strains of both   Butyrivibrio   and   Pseudobutyrivibrio   also shared a broad range of clusters of orthologous genes (COGs) (870), indicating recent evolution from a common ancestor. We also demonstrate that the carbohydrate-active enzymes (CAZymes) predominantly belong to glycosyl hydrolase (GH)2, 3, 5, 13 and 43, with numerous within family isoforms apparent, likely facilitating metabolic plasticity and resilience under dietary perturbations. This study provides a major advancement in our functional and evolutionary understanding of these important anaerobic bacteria.

中文翻译：

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Butyrivibrio 和 Pseudobutyrivibrio 基因组的系统发育系统学说明了巨大的分类多样性、开放的基因组和丰富的碳水化合物活性酶家族同种型

  Butyrivibrio  和 Pseudobutyrivibrio 在厌氧胃肠道微生物组中占主导地位，尤其是瘤胃，它们在收集膳食能量方面发挥着关键作用。在这些属中，五种瘤胃物种已被分类（  Butyrivibrio fibrisolvens 、  Butyrivibrio hangatei 、  Butyrivibrio proteoclasticus 、  Pseudobutyrivibrio ruminis 和 Pseudobutyrivibrio xylanivorans ），最近又增加了一个 Butyrivibrio  sp。添加了组。鉴于最近可用基因组的增加，我们重新研究了 Butyrivibrio 和 Pseudobutyrivibrio 的系统发育系统学和进化                  . 在 71 个基因组中，我们使用 16S rDNA 和 40 个基因标记系统发育树展示了当前六种物种名称（ P. ruminis 、 P. xylanivorans 、 B. fibrisolvens 、 Butyrivibrio  sp.、 B. hangatei 和B. proteclasticus          ） 被发现。然而，与这六个分类组中的核心基因（0.66-8.50%）相比，泛基因组分析显示出巨大的基因组变异和高丰度的辅助基因（91.50-99.34%），表明分类不正确。随后在不同核心基因截断值 (%) 和平均核苷酸同一性 (ANI) 分析下的泛基因组辅助基因组表明，在 32 个属中存在 42 个物种。基于修订后的 ANI 系统发育，对仍属于 B. fibrisolvens 、 B. hangatei 和 P. ruminis 的那些进行泛基因组分析，也显示拥有非常开放的基因组，说明即使在这些群体中也存在多样性。 Butyrivibrio 和 Pseudobutyrivibrio 的所有菌株          还共享广泛的直系同源基因（COG）簇（870），表明最近从一个共同祖先进化而来。我们还证明了碳水化合物活性酶 (CAZymes) 主要属于糖基水解酶 (GH)2、3、5、13 和 43，具有明显的许多家族同工型，可能促进饮食扰动下的代谢可塑性和恢复力。这项研究为我们对这些重要厌氧菌的功能和进化理解提供了重大进展。