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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 .    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1272-3) contains supplementary material, which is available to authorized users.

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