GENOME WATCH Genomes on Ice Julian Parkhill

NEWS & ANALYSIS

GENOME WATCH Genomes on ice Julian Parkhill

This month’s Genome Watch discusses the clade, rather than the Africa–Asia admixed study showed that the population struc- analysis of a Helicobacter pylori genome population found in modern Europeans. ture of the pathogen could be overlaid on from the preserved Copper-Age mummy Therefore, assuming that the strain isolated the population structure of its human host known as the Iceman and how ancient from the Iceman is representative of the and that the phylogenetic structure cre- genomes shed light on the history of European population at that time, these find- ated by the expansion of modern humans bacterial pathogens. ings set an earliest possible date for hybrid- out of Africa mirrored the structure of the ization between the Asian population and phylogeny of M. tuberculosis. These data Helicobacter pylori has long been the poster- the African population, which is much more led to the hypothesis that, as with H. pylori, child of bacterial phylogeography. As H. pylori recent than previously hypothesized. M. tuberculosis had accompanied its host is predominantly transmitted vertically The analysis of bacterial DNA from on its journey of colonization across the within families and maintained long- ancient remains has a habit of overturning world, starting approximately 70,000 years term within populations, the ancestry of the previous assumptions. For example, micro- ago4. However, more recent analysis of the bacterium reflects the ancestry and demog- biologists believed that Yersinia pestis, the genome sequences of M. tuberculosis from raphy of its human host. However, H. pylori causative agent of modern plague, was also 1,000-year-old human remains in Peru pro- is one of the most recombinogenic bacte- the cause of ancient plagues such as the Black vided a calibration point deep in the M. tuber- ria known, meaning that reconstructing its Death (in the 14th–17th centuries) and the culosis phylogenetic tree. Based on this new ancestry is not simple. Nonetheless, some very Justinian plague (in the 6th–8th centuries). tree, the last common ancestor of the entire elegant studies have shown that the genetic However, historians challenged these ideas, M. tuberculosis complex was dated to less than relationships of H. pylori can be reconstructed arguing that many aspects of ancient plagues 6,000 years ago, suggesting that although this and that these relationships recapitulate the did not fit the epidemiology of Y. pestis and pathogen may well have come out of Africa, early migrations of humans out of Africa, fol- that other agents, such as haemorrhagic it is unlikely to have done so with the early lowed by subsequent population movements viruses, must have been the cause of those radiations of modern humans5. related to events such as colonial expansion ancient plagues. The recovery of ancient Collectively, these studies demonstrate and the slave trade1. bacterial genomes from skeletons associ- that as our expertise at recovering and ana- Although these studies enabled the map- ated with the Black Death, and more recently lysing ancient DNA grows, our ability to date ping and dating of H. pylori expansions out the Justinian plague3, has shown that Y. pestis bacterial ancestry accurately will also grow, of Africa by correlation with the archaeo- was indeed the cause of those plagues. which will further our understanding of the logical dates of human migrations, one mys- Furthermore, these studies demonstrated emergence and spread of bacterial pathogens. tery remained: H. pylori infecting modern that Y. pestis repeatedly emerged from China. Julian Parkhill is at the Sanger Institute, Europeans and their diaspora seemed to be a In an interesting parallel to the phylo Wellcome Trust Genome Campus, Hinxton, hybrid of older bacterial populations from Asia geography studies of H. pylori, a genomic Cambridge CB10 1SA, UK. and Africa, although it was unclear when this study of a large global collection of [email protected] hybridization had occurred, with estimates Mycobacterium tuberculosis elucidated the doi:10.1038/nrmicro.2016.13 Published online 8 Feb 2016 between 10,000–50,000 years ago. Now, ana emergence and spread of tuberculosis. This 1. Falush, D. et al. Traces of human migrations in lysis of a H. pylori genome from the ‘Iceman’ Helicobacter pylori populations. Science 299, provides new insight into this problem. 1582–1585 (2003). 2. Maixner, F. et al. The 5300‑year-old Helicobacter pylori The Iceman is a remarkable mummy of a genome of the Iceman. Science 351, 162–165 (2016). man from southern Europe who died at high 3. Wagner, D. M. et al. Yersinia pestis and the plague of Justinian 541–543 AD: a genomic analysis. Lancet altitude in the Alps, and whose remains were Infect. Dis. 14, 319–326 (2014). preserved in the ice for 5,300 years, until their 4. Comas, I. et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with discovery in 1991. A recent paper described modern humans. Nat. Genet. 45, 1176–1182 the sequencing of H. pylori from the stomach (2013). 2 5. Bos, K. I. et al. Pre-Columbian mycobacterial genomes and gastrointestinal tract of the mummy and reveal seals as a source of New World human showed that the Iceman was colonized by a tuberculosis. Nature 514, 494–497 (2014).

single H. pylori strain. Notably, this strain was Competing interests statement from the older population related to the Asian The author declares no competing interests.