School of Microbiology, University College Cork, Cork, Ireland.
APC Microbiome Institute, University College Cork, Cork, Ireland.
Appl Environ Microbiol. 2018 Aug 17;84(17). doi: 10.1128/AEM.00993-18. Print 2018 Sep 1.
The genus includes over 200 species that are widely used in fermented food preservation and biotechnology or that are explored for beneficial effects on health. Naming, classifying, and comparing lactobacilli have been challenging due to the high level of phenotypic and genotypic diversity that they display and because of the uncertain degree of relatedness between them and associated genera. The aim of this study was to investigate the feasibility of dividing the genus into more homogeneous genera/clusters, exploiting genome-based data. The relatedness of 269 species belonging primarily to the families and was investigated through phylogenetic analysis (by the use of ribosomal proteins and housekeeping genes) and the assessment of the average amino acid identity (AAI) and the percentage of conserved proteins (POCP). For each subgeneric group that emerged, conserved signature genes were identified. Both distance-based and sequence-based metrics showed that the genus was paraphyletic and revealed the presence of 10 methodologically consistent subclades, which were also characterized by a distinct distribution of conserved signature orthologues. We present two ways to reclassify lactobacilli: a conservative division into two subgeneric groups based on the presence/absence of a key carbohydrate utilization gene or a more radical subdivision into 10 groups that satisfy more stringent criteria for genomic relatedness. Lactobacilli have significant scientific and economic value, but their extraordinary diversity means that they are not robustly classified. The 10 homogeneous genera/subgeneric entities that we identify here are characterized by uniform patterns of the presence/absence of specific sets of genes which offer potential as discovery tools for understanding differential biological features. Reclassification/subdivision of the genus into more uniform taxonomic nuclei will also provide accurate molecular markers that will be enabling for regulatory approval applications. Reclassification will facilitate scientific communication related to lactobacilli and prevent misidentification issues, which are still the major cause of mislabeling of probiotic and food products reported worldwide.
该属包括 200 多种广泛用于发酵食品保存和生物技术的物种，或用于探索对健康有益的影响。由于其表现出的高度表型和基因型多样性，以及它们与相关属之间的亲缘关系不确定，对乳杆菌进行命名、分类和比较一直具有挑战性。本研究旨在通过基于基因组的数据，探讨将该属分为更同质的属/聚类的可行性。通过系统发育分析（使用核糖体蛋白和看家基因）和评估平均氨基酸同一性 (AAI) 和保守蛋白百分比 (POCP)，对主要属于 和 科的 269 种属进行了相关性研究。对于每个出现的亚属群，都确定了保守的特征基因。基于距离和基于序列的指标均表明， 属是并系的，并揭示了存在 10 个方法上一致的亚分支，这些分支还具有独特的保守特征同源物分布特征。我们提出了两种重新分类乳杆菌的方法：基于关键碳水化合物利用基因的存在/缺失，将乳杆菌保守地分为两个亚属群，或根据更严格的基因组相关性标准，更激进地分为 10 个群。乳杆菌具有重要的科学和经济价值，但它们的巨大多样性意味着它们不能被准确分类。我们在这里确定的 10 个同质属/亚属实体具有特定基因集的存在/缺失的统一模式，这为理解差异生物特征提供了潜在的发现工具。将 属重新分类为更统一的分类核，也将提供准确的分子标记，这将为监管批准申请提供便利。重新分类将有助于与乳杆菌相关的科学交流，并防止仍然是全球报告的益生菌和食品产品错误标签的主要原因的错误鉴定问题。
