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An African origin for the intimate association between humans and Helicobacter pylori


Infection of the stomach by Helicobacter pylori is ubiquitous among humans. However, although H. pylori strains from different geographic areas are associated with clear phylogeographic differentiation1,2,3,4, the age of an association between these bacteria with humans remains highly controversial5,6. Here we show, using sequences from a large data set of bacterial strains that, as in humans, genetic diversity in H. pylori decreases with geographic distance from east Africa, the cradle of modern humans. We also observe similar clines of genetic isolation by distance (IBD) for both H. pylori and its human host at a worldwide scale. Like humans, simulations indicate that H. pylori seems to have spread from east Africa around 58,000 yr ago. Even at more restricted geographic scales, where IBD tends to become blurred, principal component clines in H. pylori from Europe strongly resemble the classical clines for Europeans described by Cavalli-Sforza and colleagues7. Taken together, our results establish that anatomically modern humans were already infected by H. pylori before their migrations from Africa and demonstrate that H. pylori has remained intimately associated with their human host populations ever since.

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Figure 1: Five ancestral populations in H. pylori.
Figure 2: Parallel geographic patterns of genetic diversity in humans and H. pylori.
Figure 3: Similar clinal gradients between principal components 1–3 from European H. pylori and humans.


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We acknowledge the receipt of bacterial strains from A. van der Ende, M. J. Blaser, N. J. Saunders, R. J. Owen, F. Mégraud and sequences from K. T. Momynaliev and C. Kraft. We thank J. Goudet for providing a modified version of FSTAT able to deal with the large data set and help with R by K. -P. Pleissner. Grant support was from the German Federal Ministry for Education and Research (BMBF) in the framework of the PathoGenoMik Network (M.A., S.S.), the Biotechnology and Biological Sciences Research Council (F.B.), the Swedish Research council (T.W.) and Lund University Hospital (T.W.)

EMBL accession numbers for DNA sequences, AM413111–418360

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Correspondence to François Balloux, Sebastian Suerbaum or Mark Achtman.

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EMBL accession numbers for DNA sequences, AM413111–418360. Reprints and permissions information is available at The authors declare no competing financial interests.

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This file contains Supplementary Figures S1-S6, Supplementary Methods, Supplementary Tables S1-S6 and additional references. (PDF 2386 kb)

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Linz, B., Balloux, F., Moodley, Y. et al. An African origin for the intimate association between humans and Helicobacter pylori. Nature 445, 915–918 (2007).

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