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The situation is cardinally different in the oral cavity. samples from approximal surfaces showing the highest diversity. Principal component analysis discriminated the profiles of the samples originating from shedding surfaces (mucosa of tongue, cheek and palate) from the samples that were obtained from solid surfaces (teeth). There was a large overlap in the higher taxa, “species-level” phylotypes and unique sequences among the three microbiomes: 84% of the Cot inhibitor-2 higher taxa, 75% of the OTUs and 65% of the unique sequences were present in at least two of the three microbiomes. The three individuals shared 1660 of 6315 unique sequences. These 1660 sequences (the “core microbiome”) contributed 66% of the reads. The overlapping OTUs contributed to 94% of the reads, while nearly all reads (99.8%) belonged to the shared higher taxa. == Conclusions == We obtained the first insight into the diversity and uniqueness of individual oral microbiomes at a resolution of next-generation sequencing. We showed that a major proportion of bacterial sequences of unrelated healthy individuals is identical, Cot inhibitor-2 supporting the concept of a core microbiome at health. == Background == The commensal human microbiome is estimated to outnumber the amount of human body cells by a factor of ten [1]. These complex microbial communities are normal residents of the skin, the oral cavity, vaginal and intestinal mucosa and carry a broad range of functions indispensable for the wellbeing of the host [2]. Usually we only become aware of their presence when the balance between the microbiota and the host is lost, and disease is manifest. This is reflected in the ample knowledge on the human microbiome at the state of disease as opposed to the limited picture we have of the healthy microbiome. In order to diagnose and treat disease at an early and reversible stage one needs to describe the commensal microbiome associated with health. For example, understanding changes in the oral microbiome at the early stages of periodontitis and dental caries, the most prevalent chronic oral diseases, would allow diagnosis and treatment before the appearance of periodontal pockets or dental hard tissue loss. Recent advances in sequencing technology, such as 454 pyrosequencing provides hundreds of thousands of nucleotide sequences at a fraction of the cost of traditional methods [3]. This deep sequencing has revealed an unexpectedly high diversity of the human oral microbiome: dental plaque pooled from 98 healthy adults comprised about 10000 microbial phylotypes [4]. This is an order of magnitude higher than previously reported 700 oral microbial phylotypes as identified by cultivation or traditional cloning and sequencing [5]. Moreover, by pooling about 100 individual microbiomes and pyrosequencing these, the ecosystem still appeared undersampled: the ultimate diversity of the oral microbiome was estimated to be around 25000 phylotypes [4]. If “everything is everywhere, but, the environment selects” [6], then a healthy Cot inhibitor-2 oral microbiome Prkwnk1 should be dominated by a “core microbiome” characteristic for health. These abundant phylotypes would maintain the functional stability and homeostasis necessary for a healthy ecosystem. To date though, there is no information available on how many of the 25000 phylotypes [4] actually contribute to a single oral cavity and how common or exclusive individual oral microbiomes of unrelated healthy individuals are. The oral cavity differs from all other human microbial habitats by the simultaneous presence of two types of surfaces for microbial colonization: shedding (mucosa) and solid surfaces (teeth Cot inhibitor-2 or dentures). This intrinsic property.