Abstract

The genus Paenibacillus was originally recognized based on the 16S rRNA gene phylogeny. Recently, a standardized bacterial taxonomy approach based on a genome phylogeny has substantially revised the classification of Paenibacillus, dividing it into 23 genera. However, the metabolic differences among these groups remain undescribed. Here, genomes of 41 Paenibacillus strains comprising 25 species were sequenced, and a comparative genomic analysis was performed considering these and 187 publicly available Paenibacillus genomes to understand their phylogeny and metabolic differences. Phylogenetic analysis indicated that Paenibacillus clustered into 10 subgroups. Core genome and pan-genome analyses revealed similar functional categories among the different Paenibacillus subgroups; however, each group tended to harbor specific gene families. A large proportion of genes in the subgroups A, E, and G are related to carbohydrate metabolism. Among them, genes related to the glycoside hydrolase family were most abundant. Metabolic reconstruction of the newly sequenced genomes showed that the Embden–Meyerhof–Parnas pathway, pentose phosphate pathway, and citric acid cycle are central pathways of carbohydrate metabolism in Paenibacillus. Further, the genomes of the subgroups A and G lack genes involved in glyoxylate cycle and d-galacturonate degradation, respectively. The current study revealed the metabolic diversity of Paenibacillus subgroups assigned based on a genomic phylogeny and could inform the taxonomy of Paenibacillus.

Key points

• Paenibacillus clustered into 10 subgroups.

• Genomic content variation and metabolic diversity in the subgroup A, E, and G were described.

• Carbohydrate transport and metabolism is important for Paenibacillus survival.

中文翻译：

---

比较基因组分析揭示了不同Paenibacillus组的代谢多样性

摘要

Paenibacillus属最初是根据16S rRNA基因系统发育来识别的。最近，基于基因组系统发育的标准化细菌分类学方法已对Paenibacillus的分类进行了实质性修改，将其分为23个属。但是，这些组之间的代谢差异仍未描述。在此，对包括25个物种的41株Paenibacillus菌株的基因组进行了测序，并针对这些基因组和187个公开可用的Paenibacillus基因组进行了比较基因组分析，以了解它们的系统发生和代谢差异。系统发育分析表明，芽孢杆菌分为10个子组。核心基因组和泛基因组分析揭示了不同的Paenibacillus亚组之间相似的功能类别。然而，每个群体倾向于带有特定的基因家族。A，E和G子组中的大部分基因与碳水化合物代谢有关。其中，与糖苷水解酶家族相关的基因最丰富。新测序基因组的代谢重建显示，Embden–Meyerhof–Parnas途径，磷酸戊糖途径和柠檬酸循环是Paenibacillus碳水化合物代谢的主要途径。此外，亚组A和G的基因组缺少乙醛酸循环和d涉及的基因-半乳糖醛酸酯降解。目前的研究表明，根据基因组系统发育划分的芽孢杆菌亚组的代谢多样性，可以指导芽孢杆菌的分类学。

关键点

•芽孢杆菌分为10个亚组。

•描述了A，E和G亚组的基因组含量变化和代谢多样性。

•碳水化合物的运输和代谢对于Paenibacillus的生存很重要。