Identification and Classification for the Lactobacillus casei Group.
Identification and Classification for the Lactobacillus casei Group.
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DOI：
10.3389/fmicb.2018.01974
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发表时间：
2018
影响因子：
5.2
通讯作者：
Watanabe K
中科院分区：
文献类型：
--
作者：
Huang CH;Li SW;Huang L;Watanabe K
干酪乳杆菌、副干酪乳杆菌和鼠李糖乳杆菌在表型和基因型上密切相关，共同构成干酪乳杆菌组。尽管该组菌株作为益生菌具有商业价值，但干酪乳杆菌组的分类地位和命名长期以来一直存在争议，因为使用最常用的 16S rRNA 基因测序的基因型方法来鉴定这三个物种很困难。 DNA-DNA 杂交长期以来被用作物种分类的黄金标准，但它非常费力，需要专业技能，并且很难在实验室中常规使用。目前，基于基因组的比较，包括平均核苷酸同一性 (ANI) 和数字 DNA-DNA 杂交 (dDDH)，通常应用于细菌分类学，作为划分系统发育关系的金标准方法的替代方法。为了建立在物种和亚种水平上快速准确地鉴定干酪乳杆菌组菌株的方法，我们开发了基于管家基因序列和全细胞基质辅助激光解吸/电离飞行时间质谱（MALDI-TOF MS）光谱图谱分析的物种和亚种特异性鉴定方法。通过基于串联管家基因序列（dnaJ、dnaK、mutL、pheS 和 yycH）的系统发育分析，将 53 个菌株分为四个簇，分别对应四个物种：干酪乳杆菌、副干酪乳杆菌和鼠李糖乳杆菌，以及嘉年华乳杆菌。十一月使用基于 dnaK 基因序列的单核苷酸多态性 (SNP) 特异性引物和基于 mutL 基因序列的物种特异性引物的多重小测序测定提供了高分辨率，使得能够在物种水平上将菌株鉴定为干酪乳杆菌、副干酪乳杆菌和鼠李糖乳杆菌。通过 MALDI-TOF MS 分析，结合内部数据库和 ClinProTools 软件，根据可靠的评分以及物种和亚种特异性 MS 峰，鉴定了物种和亚种级别的干酪乳杆菌组菌株。根据亚种特异性 MS 峰，可以在亚种水平上清楚地区分副干酪乳杆菌菌株。本文介绍了基于管家基因序列和MALDI-TOF MS分析的干酪乳杆菌类群菌株快速、准确的鉴定和分类方法，以及包括嘉义乳杆菌在内的该类群的新物种形态。十一月和基于基因组方法的“玉米乳杆菌”。
Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA–DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories. Currently, genome-based comparisons, including average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), are commonly applied to bacterial taxonomy as alternatives to the gold standard method for the demarcating phylogenetic relationships. To establish quick and accurate methods for identifying strains in the L. casei group at the species and subspecies levels, we developed species- and subspecies-specific identification methods based on housekeeping gene sequences and whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis. By phylogenetic analysis based on concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, and yycH), 53 strains were separated into four clusters corresponding to the four species: L. casei, L. paracasei and L. rhamnosus, and Lactobacillus chiayiensis sp. nov. A multiplex minisequencing assay using single nucleotide polymorphism (SNP)-specific primers based on the dnaK gene sequences and species-specific primers based on the mutL gene sequences provided high resolution that enabled the strains at the species level to be identified as L. casei, L. paracasei, and L. rhamnosus. By MALDI-TOF MS analysis coupled with an internal database and ClinProTools software, species- and subspecies-level L. casei group strains were identified based on reliable scores and species- and subspecies-specific MS peaks. The L. paracasei strains were distinguished clearly at the subspecies level based on subspecies-specific MS peaks. This article describes the rapid and accurate methods used for identification and classification of strains in the L. casei group based on housekeeping gene sequences and MALDI-TOF MS analysis as well as the novel speciation of this group including L. chiayiensis sp. nov. and ‘Lactobacillus zeae’ by genome-based methods.
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影响因子：
--
作者：
Auch AF;von Jan M;Klenk HP;Göker M
通讯作者：
Göker M
影响因子：
2.4
作者：
Doan, N. T. L.;Van Hoorde, K.;Vandamme, P.
通讯作者：
Vandamme, P.
DOI：
10.1099/ijs.0.030619-0
发表时间：
2012-03-01
影响因子：
2.8
作者：
Chao, Shiou-Huei;Kudo, Yuko;Watanabe, Koichi
通讯作者：
Watanabe, Koichi
影响因子：
0.7
作者：
Callaway, Angelika;Kostrzewa, Markus;Kneist, Susanne
通讯作者：
Kneist, Susanne
DOI：
10.1099/00207713-46-1-337
发表时间：
1996-01-01
期刊：
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY
影响因子：
--
作者：
Dicks, LMT;DuPlessis, EM;Lauer, E
通讯作者：
Lauer, E