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Development of new classification system for pathogenic Nocardia based on whole genome sequences and microarray analysis

基于全基因组序列和微阵列分析的致病性诺卡氏菌新分类系统的开发

基本信息

批准号：
17590385
负责人：
MIKAMI Yuzuru
金额：
$ 2.18万
依托单位：
Chiba University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
2005
资助国家：
日本
起止时间：
2005 至 2006
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-17590385/
关键词：
Nocardia new classification system gryB gene genome 16S rDNA siderophore 種の鑑別法

项目摘要

We reported the genomic sequence of Nocardia farcinica IFM 10152 in 2004. Based on the sequence, we found and analyzed genes which were specific to this species. DNA of size 238 bp specific to N. farcinica was selected for further studies. A section of this DNA partially encoded a hypothetical protein (nfa 29510), and the remaining was a non-coding region located next to a membrane protein (nfa 29520) gene. From these genetic analyses, a specific PCR primer for N. farcinica strains was designed, and their specificity was confirmed. In addition, the primer was found to be useful for the detection of N. farcinica in the blood of mice with experimental nocardiosis. The primer was also found to be useful for RealTime PCR.Based on the sequence of gyrB gene from N. farcinica IFM 10152, a modified PCr primer for the efficient amplification of the gene in Nocardia was designed. The gyrB gene sequences of all 60 Nocardia type species were analyzed, and a phylogenetic tree was constructed. This allowed the Nocardia species to be clearly differentiated from Mycobacterium and Rhodococcus, with homogeneity values of 82% and 76%, respectively.In bacterial classification, sequence of 16S rDNA is most commonly used, with no exception in Nocardia. As for the width of difference among the 60 Nocardia species, their values are distributed from 94.5 to 100.0%. However, in gyrB which we analyzed, this difference markedly increased to 82.4 to 99.9%. Usefulness of gyrB sequence for the classification of these species was confirmed, and we proposed it as a new classification system n Nocardia. Although 1,200 bp sequence of gyrB was used in the present study, further work is in progress for the development of a system using less than 600 bp from variation domains in the gene.

2004年，我们报道了法氏诺卡氏菌IFM 10152的基因组序列。根据测序结果，我们发现并分析了该物种特有的基因。本研究选取了华南星天牛特有的238bp DNA进行了进一步的研究。该片段部分编码一个假想蛋白(NfA 29510)，其余部分为非编码区，位于膜蛋白基因(NfA 29520)旁边。在这些遗传分析的基础上，设计了一条针对华南星天牛菌株的特异的聚合酶链式反应引物，并证实了其特异性。此外，还发现该引物可用于检测实验性诺卡氏菌病小鼠血液中的法氏不动杆菌。根据华南诺卡氏菌IFM 10152的gyrB基因序列，设计了一种能有效扩增诺卡氏菌gyrB基因的改进的聚合酶链式反应引物。对所有60种诺卡氏菌的gyrB基因序列进行了分析，并构建了系统发育树。在细菌分类中，16S rDNA序列是最常用的，诺卡氏菌也不例外。60种诺卡氏菌的差异幅度分布在94.5-100.0%之间。然而，在我们分析的gyrB中，这一差异显著增加到82.4%至99.9%。GyrB序列在这些种的分类中是有用的，我们建议将其作为诺卡氏菌的一个新的分类系统。虽然在本研究中使用了gyrB的1200bp的序列，但进一步的工作正在进行中，以开发一种使用该基因变异区域中少于600bp的系统。

项目成果

期刊论文数量（22）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Gorodnia otitidis sp. nov., isolated from a patient with external otitis

Gorodnia otitidis sp。

DOI：
发表时间：
2005
期刊：
International Journal of Systematic and Evolutionary Microbiology 55
影响因子：
0
作者：
Iida S;et al.
通讯作者：
et al.

Nocardia terpenica sp nov., isolated from Japanese patients with nocardiosis

DOI：
10.1099/ijs.0.64695-0
发表时间：
2007-07-01
期刊：
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
影响因子：
2.8
作者：
Hoshino, Yasutaka;Watanabe, Kayo;Mikami, Yuzuru
通讯作者：
Mikami, Yuzuru

Nocardia exalbida sp nov., isolated from Japanese patients with nocardiosis

DOI：
10.1099/ijs.0.63850-0
发表时间：
2006-06-01
期刊：
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
影响因子：
2.8
作者：
Lida, Soji;Kageyama, Akiko;Mikami, Yuzuru
通讯作者：
Mikami, Yuzuru

Construction of a pair of practical Nocardia-Escherichia coli shuttle vectors.

DOI：
10.7883/yoken.jjid.2007.45
发表时间：
2007-02
期刊：
Japanese journal of infectious diseases
影响因子：
2.2
作者：
K. Chiba;Y. Hoshino;K. Ishino;Takahisa Kogure;Y. Mikami;Y. Uehara;J. Ishikawa
通讯作者：
K. Chiba;Y. Hoshino;K. Ishino;Takahisa Kogure;Y. Mikami;Y. Uehara;J. Ishikawa

Biotransformation of bile acids by pathogenic Nocardia otitidiscaviarum and Amycolatopsis sp. strains

致病性诺卡氏菌和拟无枝酸菌对胆汁酸的生物转化。