Dhakal Rajat, Seale R Brent, Deeth Hilton C, Craven Heather, Turner Mark S
School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia.
Appl Environ Microbiol. 2014 Jun;80(11):3453-62. doi: 10.1128/AEM.00065-14. Epub 2014 Mar 21.
The spore-forming bacterium Bacillus licheniformis is a common contaminant of milk and milk products. Strains of this species isolated from dairy products can be differentiated into three major groups, namely, G, F1, and F2, using random amplification of polymorphic DNA (RAPD) analysis; however, little is known about the genomic differences between these groups and the identity of the fragments that make up their RAPD profiles. In this work we obtained high-quality draft genomes of representative strains from each of the three RAPD groups (designated strain G-1, strain F1-1, and strain F2-1) and compared them to each other and to B. licheniformis ATCC 14580 and Bacillus subtilis 168. Whole-genome comparison and multilocus sequence typing revealed that strain G-1 contains significant sequence variability and belongs to a lineage distinct from the group F strains. Strain G-1 was found to contain genes coding for a type I restriction modification system, urease production, and bacitracin synthesis, as well as the 8-kbp plasmid pFL7, and these genes were not present in strains F1-1 and F2-1. In agreement with this, all isolates of group G, but no group F isolates, were found to possess urease activity and antimicrobial activity against Micrococcus. Identification of RAPD band sequences revealed that differences in the RAPD profiles were due to differences in gene lengths, 3' ends of predicted primer binding sites, or gene presence or absence. This work provides a greater understanding of the phylogenetic and phenotypic differences observed within the B. licheniformis species.
产芽孢细菌地衣芽孢杆菌是牛奶和奶制品中常见的污染物。利用随机扩增多态性DNA(RAPD)分析,从乳制品中分离出的该物种菌株可分为三个主要组,即G组、F1组和F2组;然而,关于这些组之间的基因组差异以及构成其RAPD图谱的片段的身份知之甚少。在这项工作中,我们获得了来自三个RAPD组中每个组的代表性菌株(分别命名为菌株G-1、菌株F1-1和菌株F2-1)的高质量基因组草图,并将它们相互比较,同时与地衣芽孢杆菌ATCC 14580和枯草芽孢杆菌168进行比较。全基因组比较和多位点序列分型显示,菌株G-1含有显著的序列变异性,属于与F组菌株不同的谱系。发现菌株G-1含有编码I型限制修饰系统、脲酶产生和杆菌肽合成的基因,以及8-kbp质粒pFL7,而这些基因在菌株F1-1和F2-1中不存在。与此一致的是,发现所有G组分离株都具有脲酶活性和对微球菌的抗菌活性,而F组分离株则没有。RAPD条带序列的鉴定表明,RAPD图谱的差异是由于基因长度、预测引物结合位点的3'端或基因的存在与否不同所致。这项工作有助于更深入地了解在地衣芽孢杆菌物种中观察到的系统发育和表型差异。