title: Comparative genome analysis of Prevotella intermedia strain isolated from infected root canal reveals features related to pathogenicity and adaptation.
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.
authors.affiliation: 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.|Shanghai Institutes of Pilot Genomics and Human Health, Shanghai, 200030, China. ryf.alexandria@gmail.com.
authors.forename: Yunfeng
authors.initials: Y
authors.lastname: Ruan
authors.affiliation: 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.|Shanghai Institutes of Pilot Genomics and Human Health, Shanghai, 200030, China. mailer.shen@gmail.com.
authors.forename: Lu
authors.initials: L
authors.lastname: Shen
authors.affiliation: Department of Endodontics, 9th People's Hospital, Shanghai JiaoTong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China. zouyan1119@163.com.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zou
authors.affiliation: Department of Endodontics, 9th People's Hospital, Shanghai JiaoTong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China. qizhengnan7@sina.cn.
authors.forename: Zhengnan
authors.initials: Z
authors.lastname: Qi
authors.affiliation: Department of Endodontics, 9th People's Hospital, Shanghai JiaoTong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China. yjzaish@sohu.com.
authors.forename: Jun
authors.initials: J
authors.lastname: Yin
authors.affiliation: 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.
authors.forename: Jie
authors.initials: J
authors.lastname: Jiang
authors.affiliation: The Fourth Hospital of Jinan City; Taishan Medical College, Jinan, 250031, China. gl_5656@163.com.
authors.forename: Liang
authors.initials: L
authors.lastname: Guo
authors.affiliation: 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.|Shanghai Institutes of Pilot Genomics and Human Health, Shanghai, 200030, China. helinhelin@gmail.com.
authors.forename: Lin
authors.initials: L
authors.lastname: He
authors.affiliation: 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.|Center for Reproductive Medicine, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China. chenzijiang@hotmail.com.
authors.forename: Zijiang
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Department of Endodontics, 9th People's Hospital, Shanghai JiaoTong University, School of Medicine, Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China. tangzisheng163@163.com.
authors.forename: Zisheng
authors.initials: Z
authors.lastname: Tang
authors.affiliation: 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.|Shanghai Institutes of Pilot Genomics and Human Health, Shanghai, 200030, China. chinsir@sjtu.edu.cn.
authors.forename: Shengying
authors.initials: S
authors.lastname: Qin
mesh_terms: D000328:Adult; D000818:Animals; D001426:Bacterial Proteins / Q000235:genetics; D001430:Bacteriocins / Q000378:metabolism; D055028:Comparative Genomic Hybridization; D020451:Contig Mapping; D004247:DNA / Q000737:chemistry / Q000302:isolation & purification; D003786:Dental Pulp Cavity / Q000382:microbiology*; D024881:Drug Resistance, Bacterial / Q000235:genetics; D004912:Erythrocytes / Q000378:metabolism; D016680:Genome, Bacterial; D006461:Hemolysis; D006801:Humans; D007501:Iron / Q000378:metabolism; D008297:Male; D008962:Models, Theoretical; D005810:Multigene Family; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D018713:Prevotella intermedia / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D017422:Sequence Analysis, DNA; D037521:Virulence Factors / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D001430:Bacteriocins; D037521:Virulence Factors; D004247:DNA; D007501:Iron