BACKGROUND: The microbiota colonizing dental implants has been said to be similar to the microbiome surrounding teeth. In the absence of inflammation, a biofilm with pathologic bacteria can cover implant surfaces exposed to the oral cavity, for example, due to a remodeling process. The aim of the present study is to identify microbiota surrounding exposed dental implants in patients with and without a history of periodontitis through a deep-sequencing approach. METHODS: An experimental abutment with the same surface and structure as a commercially available dental implant was used. Bacterial DNA was isolated, and the 16S ribosomal RNA gene was amplified and sequenced. Multiplexed tag-encoded sequencing of DNA from the samples was performed, and the reads were processed by metagenomic rapid annotation. RESULTS: A wide variety of bacteria, 96 species, were identified. The most frequently found bacteria were Fusobacterium nucleatum and Prevotella denticola. Some species generally associated with periodontitis were found to a greater extent in patients without a history of periodontitis. Some bacteria that have never been described as part of the oral microbiome were identified in the present sample. CONCLUSIONS: Analysis of data suggests that the bacteria surrounding exposed dental implants form a diverse microbiome regardless of the periodontal profile of patients. Further research is needed to clarify the role of these microorganisms in the oral environment.