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Background  To investigate the microbial composition of biofilms at inflamed peri-implant and periodontal tissues in the same subject, using 16S rRNA sequencing.    Methods  Supra- and submucosal, and supra- and subgingival plaque samples were collected from 7 subjects suffering from diseased peri-implant and periodontal tissues. Bacterial DNA was isolated and 16S rRNA genes were amplified, sequenced and aligned for the identification of bacterial genera.    Results  43734 chimera-depleted, denoised sequences were identified, corresponding to 1 phylum, 8 classes, 10 orders, 44 families and 150 genera. The most abundant families or genera found in supramucosal or supragingival plaque were  Streptoccocaceae, Rothia  and  Porphyromonas.  In submucosal plaque, the most abundant family or genera found were  Rothia, Streptococcaceae  and  Porphyromonas  on implants. The most abundant subgingival bacteria on teeth were  Prevotella, Streptococcaceae,  and  TG5.  The number of sequences found for the genera  Tannerella  and  Aggregatibacter  on implants differed significantly between supra- and submucosal locations before multiple testing. The analyses demonstrated no significant differences between microbiomes on implants and teeth in supra- or submucosal and supra- or subgingival biofilms.    Conclusion  Diseased peri-implant and periodontal tissues in the same subject share similiar bacterial genera and based on the analysis of taxa on a genus level biofilm compositions may not account for the potentially distinct pathologies at implants or teeth.    Electronic supplementary material  The online version of this article (doi:10.1186/1472-6831-14-157) contains supplementary material, which is available to authorized users.

Pyrosequencing of supra- and subgingival biofilms from inflamed peri-implant and periodontal sites