An ancient ecospecies ofHelicobacter pylorifound in Indigenous populations and animal adapted lineages

Abstract

AbstractThe colonization of our stomachs byHelicobacter pyloriis believed to predate the oldest splits between extant human populations. We identify a “Hardy” ecospecies ofH. pyloriassociated with indigenous groups, isolated from people in Siberia, Canada, and USA. The ecospecies shares the ancestry of “Ubiquitous”H. pylorifrom the same geographical region in most of the genome but has nearly fixed SNP differences in 100 genes, many of which encode outer membrane proteins and previously identified host interaction factors. For these parts of the genome, the ecospecies has a separate, independently evolving gene pool with a distinct evolutionary history.H. acinonychis, found in big cats, and a newly identified primate-associated lineage both belong to the Hardy ecospecies and both represent human to animal host jumps. Most strains from the ecospecies encode an additional iron-dependent urease that is shared byHelicobacterfrom carnivorous hosts, as well as a tandem duplication ofvacA, encoding the vacuolating toxin. We conclude thatH. pylorisplit into two highly distinct ecospecies approximately 300,000 years ago and that both dispersed around the globe with humans. Coexistence has likely been possible because the ecospecies are adapted to different host diets, but the Hardy ecospecies has gone extinct in most parts of the world. Our analysis also pushes back the likely length of the association betweenH. pyloriand humans.