窄养单胞菌属的基因组和系统发育再评价：嗜热窄养单胞菌的描述，以及11 .副窄养单胞菌、11 .假窄养单胞菌、11 .足窄养单胞菌和11 .异位窄养单胞菌的提出。

IF 3.3 2区生物学 Q2 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Systematic and applied microbiology Pub Date : 2025-06-18 DOI:10.1016/j.syapm.2025.126630

Amandine Chauviat, Danis Abrouk, Elisabeth Brothier, Daniel Muller, Thibault Meyer , Sabine Favre-Bonté

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引用次数: 0

摘要

嗜麦芽寡养单胞菌物种复合体（Smc）目前包括19个基因组物种，以其生态多样性和作为机会性人类病原体的作用而闻名。然而，菌株之间显著的基因组变异性使它们的分类变得复杂，并且在Smc中只有少数物种被有效描述。尽管连续的分类修订，仍然没有在许多基因组物种的命名上达成共识，很大程度上是由于整个复合体的表型异质性。在这项研究中，我们进行了全面的基因组和系统发育重新评估，以澄清窄养单胞菌属及其物种复合体的界限。利用全基因组系统发育和总体基因组相关指数（OGRIs），如数字DNA-DNA杂交（dDDH）、平均核苷酸身份（ANIb和ANIm）和平均氨基酸身份（AAI），我们建立了精确的截断值来定义属和Smc。我们的分析导致了窄养单胞菌属的正式修订，导致了四个新的细菌属的描述：同种窄养单胞菌gen. Nov、养足单胞菌gen. Nov、副窄养单胞菌gen. Nov和伪窄养单胞菌gen. Nov。此外，我们通过确定每个基因组种的参考菌株，在Smc内标准化了命名法。其中，我们描述了一个新种，嗜热窄养单胞菌sp. nov（型菌株BurA1T = LMG 33562T = EML 1882T）。本研究为今后窄养单胞菌属的分类学和生态学研究提供了一个强有力的框架。

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Genomic and phylogenetic re-assessment of the genus Stenotrophomonas: Description of Stenotrophomonas thermophila sp. nov., and the proposal of Parastenotrophomonas gen. Nov., Pseudostenotrophomonas gen. Nov., Pedostenotrophomonas gen. Nov., and Allostenotrophomonas gen. Nov.

The Stenotrophomonas maltophilia species complex (Smc) currently comprises 19 genomospecies, known for their ecological versatility and role as opportunistic human pathogens. However, significant genomic variability among strains has complicated their classification, and only a few species within the Smc have been validly described. Despite successive taxonomic revisions, there remains no consensus on the naming of many genomospecies, largely due to the phenotypic heterogeneity across the complex.

In this study, we performed a comprehensive genomic and phylogenetic re-assessment to clarify the boundaries of the Stenotrophomonas genus and its species complex. Using whole-genome phylogeny and Overall Genome-Related Indices (OGRIs) such as digital DNA-DNA hybridization (dDDH), Average Nucleotide Identity (ANIb and ANIm), and Average Amino Acid Identity (AAI), we established precise cutoffs for defining the genus and the Smc. Our analysis led to the formal revision of the Stenotrophomonas genus, resulting in the delineation of four novel bacterial genera: Allostenotrophomonas gen. Nov., Pedostenotrophomonas gen. Nov., Parastenotrophomonas gen. Nov., and Pseudostenotrophomonas gen. Nov. Additionally, we standardized the nomenclature within the Smc by identifying reference strains for each genomospecies. Among these, we describe a novel species, Stenotrophomonas thermophila sp. nov. (type strain BurA1^T = LMG 33562^T = EML 1882^T). This study provides a robust framework for future taxonomic and ecological studies within the Stenotrophomonas genus.

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来源期刊

Systematic and applied microbiology 生物-生物工程与应用微生物

CiteScore

7.50

自引率

5.90%

发文量

审稿时长

22 days

期刊介绍： Systematic and Applied Microbiology deals with various aspects of microbial diversity and systematics of prokaryotes. It focuses on Bacteria and Archaea; eukaryotic microorganisms will only be considered in rare cases. The journal perceives a broad understanding of microbial diversity and encourages the submission of manuscripts from the following branches of microbiology: