<i>Helicobacter pylori</i> Sequences Reflect Past Human Migrations

Abstract

The long association between the stomach bacterium Helicobacter pylori and humans, in combination with its predominantly within-family transmission route and its exceptionally high DNA sequence diversity, make this bacterium a reliable marker for discerning both recent and ancient human population movements. As much of the diversity in H. pylori sequences is generated by recombination and mutation on a local scale, the partitioning of H. pylori sequences from a large globally distributed data set into six geographic populations enabled the detection of recent ( < 500 years) human population movements including the European colonial expansion and the slave trade. The further separation of bacterial populations into distinct sub-populations traced prehistoric population movements like the settlement of the Americas by Asians across the Bering Strait and the Bantu migrations in Africa. The ability to deduce ancestral population structure from modern sequences was a key development that allowed the detection of zones of admixture, such as Europe, and the inference of multiple migration waves into these zones. The significantly similar global population structure of both H. pylori and humans confirmed not only an evolutionary time-scale association between host and parasite, but also that humans had carried H. pylori in their stomachs on their migrations out of Africa.

J-Western Forms of Helicobacter pylori cagA Constitute a Distinct Phylogenetic Group with a Widespread Geographic Distribution

“…MLST analysis was performed as previously described (19,37). In brief, partial nucleotide sequences of seven housekeeping genes (atpA, efp, mutY, ppa, trpC, ureI, and yphC) were compared to the corresponding sequences of 490 reference H. pylori strains that were previously classified into distinct groups (20,35,39). Nucleotide sequences of the concatenated MLST loci were aligned using the MUSCLE algorithm within MEGA5 (55).…”

“…H. pylori strains isolated from unrelated humans display a high level of genetic diversity (9,20,50), and the intraspecies recombination rate in H. pylori is higher than in most other bacteria (52). Multilocus sequence typing (MLST) has revealed multiple populations and subpopulations of strains with distinct geographic distributions (20,35,39). It has been proposed that H. pylori had an African ancestral origin and subsequently spread throughout the world concurrently with human migrations (4,25,35,50).…”

Molecular Evolution of the Helicobacter pylori Vacuolating Toxin Gene vacA

“…The population structure of H. pylori is panmictic, and the rate of recombination in H. pylori is reported to be among the highest in the Eubacteria (17,44). Multilocus sequence analysis of housekeeping genes has revealed the presence of at least nine different H. pylori populations or subpopulations that are localized to distinct geographic regions (12,27,31). Analysis of these sequences suggests that H. pylori has spread throughout the world concurrently with the major events of human dispersal, and thus H. pylori is potentially a useful marker for the geographic migrations of human populations (12).…”

Contradictions and Concordances in American Colonization Models

“…Often a benign pathogen, H. pylori is also associated with increased risk of stomach ulcers and cancer in some individuals. Unsurprisingly, sequence analysis of H. pylori among Native American samples reveals close phylogenetic association with East Asian lineages of the bacterium, reflecting the origin of this pathogen in the Americas coincident with colonization of the Americas from Asia (see also Moodley and Linz 2009). Unlike the case in other colonizing populations (e.g., Polynesians), the sequence diversity in Native American colonies of H. pylori shows no evidence for the effect of drift (Falush et al 2003), i.e., no reduction in variation due to founder effect.…”