title: Elevated levels of adaption in Helicobacter pylori genomes from Japan; a link to higher incidences of gastric cancer?
abstract: Helicobacter pylori is a bacterium that lives in the human stomach and is a major risk factor for gastric cancer and ulcers. H.pylori is host dependent and has been carried with human populations around the world after their departure from Africa. We wished to investigate how H.pylori has coevolved with its host during that time, focusing on strains from Japanese and European populations, given that gastric cancer incidence is high in Japanese populations, while low in European. A positive selection analysis of eight H.pylori genomes was conducted, using maximum likelihood based pairwise comparisons in order to maximize the number of strain-specific genes included in the study. Using the genic Ka/Ks ratio, comparisons of four Japanese H.pylori genomes suggests 25-34 genes under positive selection, while four European H.pylori genomes suggests 16-21 genes; few of the genes identified were in common between lineages. Of the identified genes which were annotated, 38% possessed homologs associated with pathogenicity and / or host adaptation, consistent with their involvement in a coevolutionary 'arms race' with the host. Given the efficacy of identifying host interaction factors de novo, in the absence of functionally annotated homologs our evolutionary approach may have value in identifying novel genes which H.pylori employs to interact with the human gut environment. In addition, the larger number of genes inferred as being under positive selection in Japanese strains compared to European implies a stronger overall adaptive pressure, potentially resulting from an elevated immune response which may be linked to increased inflammation, an initial stage in the development of gastric cancer.
authors: Bioinformatics Lab, Department of Biology, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico.
authors: Maria Juliana
authors: MJ
authors: Soto-Girón
authors: Bioinformatics Lab, Department of Biology, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico.
authors: Oscar E
authors: OE
authors: Ospina
authors: Bioinformatics Lab, Department of Biology, University of Puerto Rico - Rio Piedras, PO Box 23360, San Juan 00931, Puerto Rico stevenemassey@gmail.com.
authors: Steven Edward
authors: SE
authors: Massey
keywords: Helicobacter pylori; Ka/Ks; PAML; pairwise comparison; pathogenic factors; positive selection