Figure 1.
Schematic overview of the bioinformatics pipeline used in this study.
Figure 2.
Taxonomic profile of the non-human Iceman metagenome.
Phylogenetic assignment of the bacterial and eukaryotic rRNA reads of the Iceman’s metagenome to different phyla. Indicated in brackets are the predominant assignable genera within a phylum.
Table 1.
Assignment of bacterial rRNA reads of the Icemańs metagenome to different genera and pre-selection of human pathogenic or opportunistic pathogenic bacteria according to the NCBI Genome Project database (ftp://ftp.ncbi.nih.gov/genomes/genomeprj_archive/lproks_0.txt).
Figure 3.
Gene coverage and distribution of the validated Iceman Treponema denticola reads mapped on the 2.8 Mb large genome of T. denticola ATCC35405.
From outer to inner circles coding sequences forward and reverse are highlighted in blue, tRNA and rRNAs in red, and depicted by the green bars are the log scale coverage of mapped reads. For details on genes with mapped reads, please refer to Table S2.
Figure 4.
MapDamage analysis displaying the frequency of nucleotide misincorporations (y-axes) in SOLID reads (starting on the 5’-end, x-axes) of different datasets.
(A) Human reference genome (ENA Experiment Accession No.: ERX008207) (B) Human reads of the Iceman metagenome (ENA Study Accession No.: ERP001144) (C) Validated T. denticola reads from the Iceman metagenome. Grey lines indicate all possible misincorporations; G-to-A and C-to-T misincorporations are plotted in blue and red, respectively. The green lines display all possible variants of a nucleotide-to-gap position.
Figure 5.
Phylogenetic tree based on bacterial 23S rRNA genes of the genus Treponema and selected bacteria of the phylum Spirochaetes (serving as an outgroup).
The Iceman metagenome 23S rRNA contig is highlighted in bold. All sequences marked with an asterisk belong to a pathogenic or opportunistic pathogenic Treponema species. The scale bar indicates 10% estimated sequence divergence.
Figure 6.
PCR-based detection of different opportunistic oral pathogens in Iceman’s gingival tissue (1) and mouth swab (2) samples.
(A) PCR assay targeting the 16S rRNA gene of T. denticola. (B) PCR assay targeting the repetitive element IS1126 of Porphyromonas gingivalis. All assays include a PCR negative control (3) and a PCR of the DNA extraction blank (4).