Dif Guendouz, Djemouai Nadjette, Dif Imane, Meklat Atika, Zitouni Abdelghani
Département des Sciences Naturelles, École Normale Supérieure Taleb Abderrahmane de Laghouat, BP 4033, Laghouat 03000, Algeria.
Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure Cheikh Mohamed El Bachir El Ibrahimi, BP 92, Kouba, Algiers, Algeria.
Int J Syst Evol Microbiol. 2025 Jul;75(7). doi: 10.1099/ijsem.0.006841.
The genus comprises Gram-stain-negative, diazotrophic bacteria associated with soil and plant environments, whose taxonomic classification has not yet been thoroughly investigated. Although 16S rRNA gene-based phylogeny remains a useful preliminary tool, it often lacks the resolution needed for accurate species delineation. In this study, we conducted a comprehensive comparative genomic analysis encompassing all validly published species, integrating whole-genome phylogenomics, average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and other genome-based metrics to refine their classification. Phylogenetic trees constructed from 16S rRNA gene sequences and core genome alignments consistently demonstrated close genomic clustering between Red69ᵀ and RF4ᵀ, as well as between RG17ᵀ and RG2ᵀ. ANI and dDDH values for these strain pairs exceeded species delineation thresholds (>96% ANI and >70 % dDDH), strongly supporting their taxonomic unification. Despite minor phenotypic variations, genomic coherence suggests that Liu 2022 should be reclassified as Xu 2022, and Yang 2023 should be recognized as a later heterotypic synonym of Liu 2022. These findings underscore the necessity of integrating whole-genome analyses into microbial taxonomy to ensure species classifications reflect true genomic relationships.
该属包括与土壤和植物环境相关的革兰氏染色阴性、固氮细菌，其分类学分类尚未得到充分研究。尽管基于16S rRNA基因的系统发育仍然是一个有用的初步工具，但它往往缺乏准确划分物种所需的分辨率。在本研究中，我们对所有有效发表的物种进行了全面的比较基因组分析，整合了全基因组系统发育基因组学、平均核苷酸同一性（ANI）、数字DNA-DNA杂交（dDDH）和其他基于基因组的指标，以完善它们的分类。由16S rRNA基因序列和核心基因组比对构建的系统发育树一致显示，Red69ᵀ和RF4ᵀ之间以及RG17ᵀ和RG2ᵀ之间存在紧密的基因组聚类。这些菌株对的ANI和dDDH值超过了物种划分阈值（>96% ANI和>70 % dDDH），有力地支持了它们的分类学统一。尽管存在微小的表型差异，但基因组一致性表明，Liu 2022应重新分类为Xu 2022，Yang 2023应被视为Liu 2022的一个较新的异名。这些发现强调了将全基因组分析纳入微生物分类学的必要性，以确保物种分类反映真实的基因组关系。
