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

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.     

Complete genome sequence of Riemerella anatipestifer type strain (ATCC 11845)

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Complete genome sequence of Rhodospirillum rubrum type strain (S1)

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Complete genome sequence of Oceanithermus profundus type strain (506)

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Complete genome sequence of Thermomonospora curvata type strain (B9)

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Complete genome sequence of Anaerococcus prevotii type strain (PC1)

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Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4(T))

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Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139)

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Complete genome sequence of Tsukamurella paurometabola type strain (no. 33)

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Complete genome sequence of Meiothermus ruber type strain (21)

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Complete genome sequence of Paludibacter propionicigenes type strain (WB4)

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Complete genome sequence of Mahella australiensis type strain (50-1 BON)

Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella, which belongs to the family Thermoanaerobacteraceae. The species is of interest because it differs from other known anaerobic spore-forming bacteria in its G+C content, and in certain phenotypic traits, such as carbon source utilization and relationship to temperature. Moreover, it has been discussed that this species might be an indigenous member of petroleum and oil reservoirs. This is the first completed genome sequence of a member of the genus Mahella and the ninth completed type strain genome sequence from the family Thermoanaerobacteraceae. The 3,135,972 bp long genome with its 2,974 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Cellulomonas flavigena type strain (134)

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Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3)

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Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1)

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Complete genome sequence of Thermosediminibacter oceani type strain (JW/IW-1228P)

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Complete genome sequence of Cellulophaga lytica type strain (LIM-21)

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Complete genome sequence of Haliangium ochraceum type strain (SMP-2)

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Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113)

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Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1)

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