泛基因组分析鲁氏芽孢杆菌属的物种多样性与潜在工业应用

Pangenome analysis of Rummeliibacillus sp. strains reveals their unexpected diversity and potential for industrial application

摘要:

目的 鲁氏芽孢杆菌属(Rummeliibacillus)包含3个种，即R. stabekisii、R. pycnus和R. suwonensis，在生物降解、益生菌、动物饲料以及精氨酸、己酸等的生产方面具有一定的应用潜力。本研究旨在从基因组水平研究该属的遗传多样性。方法 对该属不同来源的12个菌株进行比较泛基因组分析，分析内容还包括菌株的系统发育分析、功能注释、基因组代谢途径分析以及可移动遗传元件预测。结果 泛基因组分析共鉴定出8 024个基因家族，核心基因组、附属基因组和菌株特异性基因分别包含1 550、3 941和2 533个基因家族。在核心基因组中，6个菌株的精氨酸循环是完整的，7个菌株具备完全生物合成乙偶姻的能力。然而，只有R. pycnus和R. suwonensis 3B-1具有合成己酸的能力。通过系统发育树、DNA-DNA杂交(DNA-DNA hybridization， DDH)和平均核苷酸一致性(average nucleotide identity, ANI)分析发现，Rummeliibacillus sp. G93和Rummeliibacillus sp. TYF-LIM-RU47均属于R. stabekisii。Rummeliibacillus sp. POC4和Rummeliibacillus sp. TYF005可能属于该属的一个新种。此外，在所有12个菌株中均鉴定出基因岛，其数量从4个(R. stabekisii DSM 25578和R. stabekisii NBRC 104870)到14个(Rummeliibacillus sp. SL167菌株和Rummeliibacillus sp. TYF005菌株)不等，并且在5个分析菌株发现了前噬菌体序列。结论 本研究提供了Rummeliibacillus sp.较为全面的基因家族谱，有助于对其进行进一步探索。

Abstract:

Objective Rummeliibacillus, a genus encompassing three known species, R. stabekisii, R. pycnus, and R. suwonensis, has a wide range of potential applications in biodegradation, probiotics, animal feed, and production of arginine, caproic acid, and other compounds. This study aims to explore the genetic diversity of this genus at the genomic level.Methods A comparative pangenome analysis of 12 strains isolated from different sources was conducted. In addition, the phylogenetic analysis, functional annotation, genomic metabolic pathway analysis, and prediction of mobile genetic elements were carried out.Results A total of 8 024 gene clusters were identified. The core genome, accessory genome, and strain-specific genes comprised 1 550, 3 941, and 2 533 gene clusters, respectively. In the core genome, the arginine cycle of six strains was complete. Seven strains had the ability to completely biosynthesize acetoin. However, only R. pycnus and R. suwonensis 3B-1 were able to completely biosynthesize caproic acid. The phylogenetic tree, DNA-DNA hybridization, and average nucleotide identity showed that Rummeliibacillus sp. G93 and Rummeliibacillus sp. TYF-LIM-RU47 were strains of R. stabekisii. Rummeliibacillus sp. POC4 and Rummeliibacillus sp. TYF005 may belong to a new species of this genus. In addition, genomic islands were identified in all the 12 strains, with the number ranging from four (R. stabekisii DSM 25578 and R. stabekisii NBRC 104870) to 14 (Rummeliibacillus sp. SL167 and Rummeliibacillus sp. TYF005), and prophage sequences were found in five of the 12 strains.Conclusion This study provides a genomic framework for Rummeliibacillus that could assist the further exploration of this genus.