1. Department of Molecular Biology, Max-Planck Institut für Infektionsbiologie, D-10117 Berlin, Germany
2. Theoretical and Molecular Population Genetics Group, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
3. Evolutionary Ecology Group, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
4. Department of Statistics, University of Oxford, Oxford OX1 3SY, UK
5. Génétique et Evolution des Maladies Infectieuses, UMR IRD-CNRS 2724, centre IRD de Montpellier, 911 Avenue Agropolis, BP 64501, 34394 Montpellier Cedex 05, France
6. Department of Internal Medicine and Gastroenterology, University of Pretoria, Pretoria 0002, South Africa
7. Department of Medicine–Gastroenterology, Baylor College of Medicine and Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
8. Department of Microbiology, Donostia Hospital, 20014 San Sebastian, Spain
9. Department of Laboratory Medicine, Lund University, SE22632 Lund, Sweden
10. Medizinische Hochschule Hannover, Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
11. These authors contributed equally to this work.

Correspondence to: François Balloux^2,11Sebastian Suerbaum¹⁰Mark Achtman¹ Correspondence and requests for materials should be addressed to M.A. (Email: achtman@mpiib-berlin.mpg.de), F.B. (Email: fb255@mole.bio.cam.ac.uk) or S.S. (Email: Suerbaum.Sebastian@mh-hannover.de).

Abstract

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 differentiation^{1, 2, 3, 4}, the age of an association between these bacteria with humans remains highly controversial^{5, 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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