Genome sequencing identifies Listeria fleischmannii subsp coloradonensis subsp nov., isolated from a ranch
Genome sequencing identifies Listeria fleischmannii subsp coloradonensis subsp nov., isolated from a ranch
复制标题
DOI：
10.1099/ijs.0.048587-0
复制
发表时间：
2013-09-01
影响因子：
2.8
通讯作者：
Nightingale, Kendra K.
中科院分区：
文献类型：
--
作者：
den Bakker, Henk C.;Manuel, Clyde S.;Nightingale, Kendra K.
从科罗拉多州北部的一个养牛场收集的环境样本中获得了 20 种类似李斯特菌的分离株；发现所有这些分离株都具有相同的部分 sigB 序列，表明密切相关。这些分离株与李斯特菌属成员相似，革兰氏染色阳性、短杆状、氧化酶阴性和过氧化氢酶阳性；这些分离株与弗莱施曼李斯特菌相似，因为它们在 25 摄氏度下不活动。对代表性分离株进行了 16S rRNA 基因测序，并对其中一种分离株进行了全基因组测序。还对弗莱施曼李斯特菌（菌株 LU2006-1(T)）的模式菌株的基因组进行了测序。基因组草案的大小非常相似，91% 的基因组中的平均 MUMmer 核苷酸同一性为 95.16%。基因组序列数据用于设计六基因多位点序列分析（MLSA）方案的引物。基于 (i) 近乎完整的 16S rRNA 基因、(ii) 31 个核心基因和 (iii) 6 个管家基因的系统发育说明了这些李斯特菌样分离株与李斯特菌 LU2006-1(T) 的密切关系。类李斯特菌分离株与弗莱施曼尼李斯特菌典型菌株的足够遗传差异以及不同的表型特征保证这些分离株被归类为不同种下分类群的成员，其名称为李斯特菌弗莱施曼尼亚种。科罗拉多亚种十一月被提议。模式菌株是TTU M1-001(T) (=BAA-2414(T)=DSM 25391(T))。弗莱施曼李斯特菌亚种 (Listeria fleischmannii subsp.) 的分离株。科罗拉多亚种十一月与指定亚种的不同之处在于不能利用松三糖、松二糖和蔗糖，但能够利用肌醇。结果还证明了全基因组测序的实用性，有助于在详细描述的属中识别新的分类群。弗莱施曼尼李斯特菌的两个亚种的基因组均含有推定的增强素基因；李斯特菌弗莱施曼尼亚种。科罗拉多亚种十一月基因组还编码了一种假定的杀蚊毒素。这些基因的存在表明可能适应昆虫宿主，并且需要进一步研究来探索弗莱施曼尼李斯特菌的生态位适应。
Twenty Listeria-like isolates were obtained from environmental samples collected on a cattle ranch in northern Colorado; all of these isolates were found to share an identical partial sigB sequence, suggesting close relatedness. The isolates were similar to members of the genus Listeria in that they were Gram-stain-positive, short rods, oxidase-negative and catalase-positive; the isolates were similar to Listeria fleischmannii because they were non-motile at 25 degrees C. 16S rRNA gene sequencing for representative isolates and whole genome sequencing for one isolate was performed. The genome of the type strain of Listeria fleischmannii (strain LU2006-1(T)) was also sequenced. The draft genomes were very similar in size and the average MUMmer nucleotide identity across 91 % of the genomes was 95.16%. Genome sequence data were used to design primers for a six-gene multi-locus sequence analysis (MLSA) scheme. Phylogenies based on (i) the near-complete 16S rRNA gene, (ii) 31 core genes and (iii) six housekeeping genes illustrated the close relationship of these Listeria-like isolates to Listeria fleischmannii LU2006-1(T). Sufficient genetic divergence of the Listeria-like isolates from the type strain of Listeria fleischmannii and differing phenotypic characteristics warrant these isolates to be classified as members of a distinct infraspecific taxon, for which the name Listeria fleischmannii subsp. coloradonensis subsp. nov. is proposed. The type strain is TTU M1-001(T) (=BAA-2414(T)=DSM 25391(T)). The isolates of Listeria fleischmannii subsp. coloradonensis subsp. nov. differ from the nominate subspecies by the inability to utilize melezitose, turanose and sucrose, and the ability to utilize inositol. The results also demonstrate the utility of whole genome sequencing to facilitate identification of novel taxa within a well-described genus. The genomes of both subspecies of Listeria fleischmannii contained putative enhancin genes; the Listeria fleischmannii subsp. coloradonensis subsp. nov. genome also encoded a putative mosquitocidal toxin. The presence of these genes suggests possible adaptation to an insect host, and further studies are needed to probe niche adaptation of Listeria fleischmannii.