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BMC Genomics. 2015 Feb 25;16:122. doi: 10.1186/s12864-015-1272-3.

Comparative genome analysis of Prevotella intermedia strain isolated from infected root canal reveals features related to pathogenicity and adaptation.

Ruan Y1,2, Shen L3,4, Zou Y5, Qi Z6, Yin J7, Jiang J8, Guo L9, He L10,11, Chen Z12,13, Tang Z14, Qin S15,16.

Author information

1
Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders(Ministry of Education, Shanghai Jiao Tong University, 1954 Huashang Road, Shanghai, 200030, China. ryf.alexandria@gmail.com.
2
Shanghai Institutes of Pilot Genomics and Human Health, Shanghai, 200030, China. ryf.alexandria@gmail.com.
3
Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders(Ministry of Education, Shanghai Jiao Tong University, 1954 Huashang Road, Shanghai, 200030, China. mailer.shen@gmail.com.
4
Shanghai Institutes of Pilot Genomics and Human Health, Shanghai, 200030, China. mailer.shen@gmail.com.
5
Department of Endodontics, 9th People's Hospital, Shanghai JiaoTong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China. zouyan1119@163.com.
6
Department of Endodontics, 9th People's Hospital, Shanghai JiaoTong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China. qizhengnan7@sina.cn.
7
Department of Endodontics, 9th People's Hospital, Shanghai JiaoTong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China. yjzaish@sohu.com.
8
Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders(Ministry of Education, Shanghai Jiao Tong University, 1954 Huashang Road, Shanghai, 200030, China. jiangjie0115@gmail.com.
9
The Fourth Hospital of Jinan City; Taishan Medical College, Jinan, 250031, China. gl_5656@163.com.
10
Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders(Ministry of Education, Shanghai Jiao Tong University, 1954 Huashang Road, Shanghai, 200030, China. helinhelin@gmail.com.
11
Shanghai Institutes of Pilot Genomics and Human Health, Shanghai, 200030, China. helinhelin@gmail.com.
12
Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders(Ministry of Education, Shanghai Jiao Tong University, 1954 Huashang Road, Shanghai, 200030, China. chenzijiang@hotmail.com.
13
Center for Reproductive Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China. chenzijiang@hotmail.com.
14
Department of Endodontics, 9th People's Hospital, Shanghai JiaoTong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China. tangzisheng163@163.com.
15
Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders(Ministry of Education, Shanghai Jiao Tong University, 1954 Huashang Road, Shanghai, 200030, China. chinsir@sjtu.edu.cn.
16
Shanghai Institutes of Pilot Genomics and Human Health, Shanghai, 200030, China. chinsir@sjtu.edu.cn.

Abstract

BACKGROUND:

Many species of the genus Prevotella are pathogens that cause oral diseases. Prevotella intermedia is known to cause various oral disorders e.g. periodontal disease, periapical periodontitis and noma as well as colonize in the respiratory tract and be associated with cystic fibrosis and chronic bronchitis. It is of clinical significance to identify the main drive of its various adaptation and pathogenicity. In order to explore the intra-species genetic differences among strains of Prevotella intermedia of different niches, we isolated a strain Prevotella intermedia ZT from the infected root canal of a Chinese patient with periapical periodontitis and gained a draft genome sequence. We annotated the genome and compared it with the genomes of other taxa in the genus Prevotella.

RESULTS:

The raw data set, consisting of approximately 65X-coverage reads, was trimmed and assembled into contigs from which 2165 ORFs were predicted. The comparison of the Prevotella intermedia ZT genome sequence with the published genome sequence of Prevotella intermedia 17 and Prevotella intermedia ATCC25611 revealed that ~14% of the genes were strain-specific. The Preveotella intermedia strains share a set of conserved genes contributing to its adaptation and pathogenic and possess strain-specific genes especially those involved in adhesion and secreting bacteriocin. The Prevotella intermedia ZT shares similar gene content with other taxa of genus Prevotella. The genomes of the genus Prevotella is highly dynamic with relative conserved parts: on average, about half of the genes in one Prevotella genome were not included in another genome of the different Prevotella species. The degree of conservation varied with different pathways: the ability of amino acid biosynthesis varied greatly with species but the pathway of cell wall components biosynthesis were nearly constant. Phylogenetic tree shows that the taxa from different niches are scarcely distributed among clades.

CONCLUSIONS:

Prevotella intermedia ZT belongs to a genus marked with highly dynamic genomes. The specific genes of Prevotella intermedia indicate that adhesion, competing with surrounding microbes and horizontal gene transfer are the main drive of the evolution of Prevotella intermedia.

PMID:
25765460
PMCID:
PMC4349605
DOI:
10.1186/s12864-015-1272-3
[Indexed for MEDLINE]
Free PMC Article

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