East Asian genotypes of Helicobacter pylori strains in Amerindians provide evidence for its ancient human carriage

Abstract

Phylogenies of indigenous microbes have been used as surrogates for the origins of the hosts that carry them. Conversely, polymorphisms may be used to date the spread of a microbial species when information about their host populations is available. Therefore, we examined polymorphisms in Helicobacter pylori, which persistently colonize the human stomach, to test the hypothesis that they have been ancient inhabitants of humans. Three H. pylori loci that previously have been shown to have phylogeographic affinity have been analyzed for two populations with different ethnic origins from Venezuela. In a group of Amerindian subjects from Amazonia, East Asian H. pylori genotypes were present for each of the loci examined but were absent in a mestizo population from Caracas. These findings provide evidence that H. pylori has been present in humans at least since ancestors of Amerindians migrated from Asia more than 11,000 years ago.

Fig 1.

Neighbor-joining trees of H. pylori based on sequences at three loci. Sequences are from H. pylori strains from East Asia/Pacific (green), Western countries (red), Venezuela/Puerto Ayacucho (VP, black), Venezuela/Caracas (VC, blue). (a) the vacA s region has four major allotypes: s1a, s1b, s1c, and s2. The majority of Venezuela/Puerto Ayacucho sequences are on the s1c branch on a relatively conserved subbranch or amidst the East Asian/Pacific isolates. (b) HP0638 sequences divide into two major groupings, with sequences from East Asia, the majority of Venezuela/Caracas, and one from Colombia together (Top), and the Venezuela/Caracas sequences and most Western sequences (Bottom). (c) babB sequences divide into two major groupings, with East Asia and most of Venezuela/Puerto Ayacucho (Bottom) together, and Venezuela/Caracas and Western together (Top). CH, China; TH, Thailand; J, Japan; NL, The Netherlands; PO, Portugal; NZ, Maori; AU, Australia; US, United States; PE, Peru; UK, United Kingdom; CO, Colombia; BE, Belgium; FI, Finland; IN, India. Bootstrap values >50 and branch-length indices are shown.