Exploring the microbiome of healthy and diseased peri-implant sites using Illumina sequencing

J Clin Periodontol. 2017 Dec;44(12):1274-1284. doi: 10.1111/jcpe.12788. Epub 2017 Nov 21.


Aim: To compare the microbiome of healthy (H) and diseased (P) peri-implant sites and determine the core peri-implant microbiome.

Materials and methods: Submucosal biofilms from 32 H and 35 P sites were analysed using 16S rRNA sequencing (MiSeq, Illumina), QIIME and HOMINGS. Differences between groups were determined using principal coordinate analysis (PCoA), t tests and Wilcoxon rank sum test and FDR-adjusted. The peri-implant core microbiome was determined.

Results: PCoA showed partitioning between H and P at all taxonomic levels. Bacteroidetes, Spirochetes and Synergistetes were higher in P, while Actinobacteria prevailed in H (p < .05). Porphyromonas and Treponema were more abundant in P while Rothia and Neisseria were higher in H (p < .05). The core peri-implant microbiome contained Fusobacterium, Parvimonas and Campylobacter sp. T. denticola, and P. gingivalis levels were higher in P, as well as F. alocis, F. fastidiosum and T. maltophilum (p < .05).

Conclusion: The peri-implantitis microbiome is commensal-depleted and pathogen-enriched, harbouring traditional and new pathogens. The core peri-implant microbiome harbours taxa from genera often associated with periodontal inflammation.

Keywords: DNA; dental implant; microbiome; peri-implantitis; periodontal; sequencing.

MeSH terms

  • Adult
  • Aged
  • Alveolar Bone Loss / microbiology
  • Bacteria / classification*
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • Bacterial Load
  • Base Sequence
  • Biofilms / growth & development
  • Case-Control Studies
  • DNA, Bacterial / genetics
  • DNA, Bacterial / isolation & purification
  • Dental Implants / microbiology*
  • Female
  • Humans
  • Male
  • Microbial Consortia / genetics
  • Microbiota / genetics*
  • Middle Aged
  • Peri-Implantitis / microbiology*
  • Periodontal Pocket / microbiology
  • RNA, Ribosomal, 16S / genetics


  • DNA, Bacterial
  • Dental Implants
  • RNA, Ribosomal, 16S