Ancient hominoid genome studies can be regarded by definition as metagenomic 
analyses since they represent a mixture of both hominoid and microbial sequences 
in an environment. Here, we report the molecular detection of the oral 
spirochete Treponema denticola in ancient human tissue biopsies of the Iceman, a 
5,300-year-old Copper Age natural ice mummy. Initially, the metagenomic data of 
the Iceman's genomic survey was screened for bacterial ribosomal RNA (rRNA) 
specific reads. Through ranking the reads by abundance a relatively high number 
of rRNA reads most similar to T. denticola was detected. Mapping of the 
metagenome sequences against the T. denticola genome revealed additional reads 
most similar to this opportunistic pathogen. The DNA damage pattern of 
specifically mapped reads suggests an ancient origin of these sequences. The 
haematogenous spread of bacteria of the oral microbiome often reported in the 
recent literature could already explain the presence of metagenomic reads 
specific for T. denticola in the Iceman's bone biopsy. We extended, however, our 
survey to an Iceman gingival tissue sample and a mouth swab sample and could 
thereby detect T. denticola and Porphyrimonas gingivalis, another important 
member of the human commensal oral microflora. Taken together, this study 
clearly underlines the opportunity to detect disease-associated microorganisms 
when applying metagenomics-enabled approaches on datasets of ancient human 
remains.