Raimondi Stefano, Candeliere Francesco, Amaretti Alberto, Costa Stefania, Vertuani Silvia, Spampinato Gloria, Rossi Maddalena
Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
Biogest Siteia, University of Modena and Reggio Emilia, Reggio Emilia, Italy.
Front Microbiol. 2022 Jul 25;13:897656. doi: 10.3389/fmicb.2022.897656. eCollection 2022.
is a genus of saccharolytic heterofermentative lactic acid bacteria that inhabit plant-derived matrices and a variety of fermented foods (dairy products, dough, milk, vegetables, and meats), contributing to desired fermentation processes or playing a role in food spoilage. At present, the genus encompasses 17 recognized species. In total, 216 deposited genome sequences of were analyzed, to check the delineation of species and to infer their evolutive genealogy utilizing a minimum evolution tree of Average Nucleotide Identity (ANI) and the core genome alignment. Phylogenomic relationships were compared to those obtained from the analysis of 16S rRNA, , and genes. All the phylograms were subjected to split decomposition analysis and their topologies were compared to check the ambiguities in the inferred phylogenesis. The minimum evolution ANI tree exhibited the most similar topology with the core genome tree, while single gene trees were less adherent and provided a weaker phylogenetic signal. In particular, the 16S rRNA gene failed to resolve several bifurcations and species. Based on an ANI threshold of 95%, the organization of the genus could be amended, redefining the boundaries of the species , and . Two strains currently recognized as were split into a separate lineage representing a putative species (G16), phylogenetically related to both (G18) and (G17). Differences among the four subspecies of were not pinpointed by ANI or by the conserved genes. The strains of were ascribed to two putative species, G13 and G14, the former including also all the strains presently belonging to was split into two phylogenetically related lineages, G9 and G10, putatively corresponding to separate species and both including subgroups that may correspond to subspecies. The species and were closely related but separated into different species, the latter including also strains. These results, integrating information of ANI, core genome, and housekeeping genes, complemented the taxonomic delineation with solid information on the phylogenetic lineages evolved within the genus .
是一类解糖异源发酵乳酸菌，存在于植物源基质和多种发酵食品（乳制品、面团、牛奶、蔬菜和肉类）中，对理想的发酵过程有贡献或在食品变质中起作用。目前，该属包含17个公认的物种。总共分析了216个已存档的 的基因组序列，以检查物种的划分，并利用平均核苷酸同一性（ANI）的最小进化树和核心基因组比对来推断它们的进化谱系。将系统发育关系与从16S rRNA、 和 基因分析中获得的关系进行比较。所有系统发育树都进行了分裂分解分析，并比较它们的拓扑结构以检查推断的系统发育中的模糊性。最小进化ANI树显示出与核心基因组树最相似的拓扑结构，而单基因树的一致性较差且提供的系统发育信号较弱。特别是，16S rRNA基因未能解决几个分支和 物种的问题。基于95%的ANI阈值， 属的分类可以修订，重新定义 、 和 物种的界限。目前被认为是 的两个菌株被分为一个单独的谱系，代表一个假定的物种（G16），在系统发育上与 （G18）和 （G17）相关。 的四个亚种之间的差异未通过ANI或保守基因确定。 的菌株被归为两个假定的物种，G13和G14，前者还包括目前属于 的所有菌株， 被分为两个系统发育相关的谱系，G9和G10，可能对应于不同的物种，并且都包括可能对应于亚种的亚组。 物种和 密切相关但分为不同的物种，后者还包括 菌株。这些结果整合了ANI、核心基因组和管家基因的信息，用关于在 属内进化的系统发育谱系的可靠信息补充了分类学划分。
