Laboratoire de Biologie des Systèmes Microbiens (LBSM), Ecole Normale Supérieure Cheikh Mohamed El Bachir El Ibrahimi, BP 92, Kouba, Algiers, Algeria.
Agri-Food and Biosciences Institute, Belfast, BT9 5PX, UK.
Antonie Van Leeuwenhoek. 2024 Oct 10;118(1):18. doi: 10.1007/s10482-024-02027-y.
The taxonomy of the Listeriaceae family has undergone substantial revisions, expanding the Listeria genus from 6 to 29 species since 2009. However, these classifications have relied on 16S rRNA gene sequences and conventional polyphasic taxonomy, with limited use of genomic approaches. This study aimed to employ genomic tools, including phylogenomics, Overall Genomic Relatedness Indices (OGRIs), and core-genome phylogenomic analyses, to reevaluate the taxonomy of the Listeriaceae family. The analyses involved the construction of phylogenetic and phylogenomic trees based on 16S rRNA gene sequences and core genomes from 34 type strain genomes belonging to Listeriaceae family. OGRIs, which encompass Average Amino acid Identity (AAI), core-proteome AAI (cAAI), and Percentage of Conserved Proteins (POCP), were calculated, and specific threshold values of 70%, 87%, and 72-73% were established, respectively, to delimitate genera in the Listeriaceae family. These newly proposed OGRI thresholds unveiled distinct evolutionary lineages. The outcomes of this taxonomic re-evaluation were: (i): the division of the Listeria genus into an emended Listeria genus regrouping only Listeria senso stricto species; (ii): the remaining Listeria senso lato species were transferred into three newly proposed genera: Murraya gen. nov., Mesolisteria gen. nov., and Paenilisteria gen. nov. within Listeriaceae; (iii): Brochothrix was transferred to the newly proposed family Brochothricaceae fam. nov. within the Caryophanales order; (iiii): Listeria ivanovii subsp. londonensis was elevated to the species level as Listeria londonensis sp. nov.; and (iiiii): Murraya murrayi comb. nov. was reclassified as a later heterotypic synonym of Murraya grayi comb. nov. This taxonomic framework enables more precise identification of pathogenic Listeriaceae species, with significant implications for important areas such as food safety, clinical diagnostics, epidemiology, and public health.
李斯特菌科的分类发生了重大修订，自 2009 年以来，李斯特菌属已从 6 种扩展到 29 种。然而，这些分类一直依赖于 16S rRNA 基因序列和传统的多相分类学，基因组方法的应用有限。本研究旨在利用基因组工具，包括系统发育基因组学、全基因组相关性指数（OGRI）和核心基因组系统发育分析，重新评估李斯特菌科的分类。分析涉及构建基于 16S rRNA 基因序列和 34 个李斯特菌科模式菌株基因组核心基因组的系统发育树和系统发育基因组树。计算了平均氨基酸同一性（AAI）、核心蛋白 AAI（cAAI）和保守蛋白百分比（POCP）的 OGRIs，并分别建立了 70%、87%和 72-73%的特定阈值，以划定李斯特菌科的属。这些新提出的 OGRI 阈值揭示了不同的进化谱系。这次分类学再评估的结果是：（i）将李斯特菌属分为一个经修正的李斯特菌属，仅包括李斯特菌属严格意义上的物种；（ii）其余的李斯特菌属感观宽谱种被转移到三个新提出的属中：Murraya 属、Mesolisteria 属和 Paenilisteria 属；（iii）将 Brochothrix 转移到 Caryophanales 目中新提出的 Brochothricaceae 科；（iv）李斯特菌伦敦亚种升级为李斯特菌伦敦亚种。物种李斯特菌伦敦ensis sp. nov.；以及（v）Murraya murrayi comb. nov. 被重新分类为 Murraya grayi comb. nov. 的后来的异型同义词。这个分类框架可以更准确地识别致病性李斯特菌科的物种，对食品安全、临床诊断、流行病学和公共卫生等重要领域具有重要意义。
