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The 5300-year-old Helicobacter pylori genome of the Iceman

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Science  08 Jan 2016:
Vol. 351, Issue 6269, pp. 162-165
DOI: 10.1126/science.aad2545
  • Fig. 1 H. pylori–specific reads detected in the metagenomic data sets of the Iceman’s intestine content samples.

    The color gradient displays the number of unambiguous H. pylori reads per million metagenomic reads. Control metagenomic data sets of the Iceman’s muscle tissue and of the extraction blank were included in the analysis. The different intestinal content sampling sites are marked in the radiographic image by the following symbols: asterisk, stomach content; circle, small intestine; square, upper large intestine; triangle, lower large intestine. The sampling site of the muscle control sample is highlighted in the Iceman overview picture (diamond).

  • Fig. 2 Gene coverage and distribution of the enriched and validated Iceman H. pylori reads mapped onto the 1.6 Mb large reference genome H. pylori 26695.

    The coverage plot displayed in black is superimposed onto the genomic plot. The bar on the right-hand side indicates a coverage of up to 50×. The gene coding sequences are shown in blue (positive strand) and yellow (negative strand) bars in the genomic plot. The loci of the ribosomal RNA genes, of two virulence genes (vacA and cagA), and of seven genes used for MLST analysis are highlighted in the genome plot.

  • Fig. 3 Multilocus sequence analyses.

    (A) Bayesian cluster analysis performed in STRUCTURE displays the population partitioning of hpEurope, hpAsia2, and hpNEAfrica and the Iceman’s H. pylori strain (details about the worldwide population partitioning of 1603 reference H. pylori strains are available in fig. S14). (B) STRUCTURE linkage model analysis showing the proportion of Ancestral Europe 1 (from Central Asia) and Ancestral Europe 2 (from northeast Africa) nucleotides among strains assigned to populations hpNEAfrica, hpEurope, and hpAsia2 and the Iceman’s H. pylori strain on the extreme right. The black arrows indicate the position of the three extant European hpAsia2 strains. (C) Principal component analysis of contemporary hpNEAfrica, hpEurope, and hpAsia2 strains and the Iceman’s H. pylori strain.

  • Fig. 4 Comparative whole-genome analysis.

    Co-ancestry matrix showing H. pylori population structure and genetic flux. The color in the heat map corresponds to the number of genomic motifs imported from a donor genome (column) to a recipient genome (row). The inferred tree and the H. pylori strain names are displayed on the top and left of the heat map. Strain names are colored according to the H. pylori population assignment provided in the legend below the heat map. Signs for population ancestry are highlighted in the heat map with green, blue, black, and white boxes.

Supplementary Materials

  • The 5300-year-old Helicobacter pylori genome of the Iceman

    Frank Maixner, Ben Krause-Kyora, Dmitrij Turaev, Alexander Herbig, Michael R. Hoopmann, Janice L. Hallows, Ulrike Kusebauch, Eduard Egarter Vigl, Peter Malfertheiner, Francis Megraud, Niall O’Sullivan, Giovanna Cipollini, Valentina Coia, Marco Samadelli, Lars Engstrand, Bodo Linz, Robert L. Moritz, Rudolf Grimm, Johannes Krause, Almut Nebel, Yoshan Moodley, Thomas Rattei, Albert Zink

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods
    • Figs. S1 to S17
    • Tables S1 to S13
    • Full Reference List

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