Helicobacter pylori genome evolution within the human stomach

Helicobacter pylori is characterized by a high genetic diversity due to a high mutation rate and frequent recombination. The human stomach, a complex, compartmentalized, ecological niche, is the only known natural reservoir of H. pylori. Genetic changes of H. pylori during chronic infection in vivo have been previously described by whole-genome sequencing during both early stage of infection, and long-term colonization. However, the extent of bacterial population variation inside the gastric environment has not been extensively investigated. The aim of this study was to determine the population structure of H. pylori within individual stomachs and to look for evidence of local adaptation to anatomical regions. Gastric biopsies were obtained from the antrum, corpus and fundus regions of 16 H. pylori-infected adults. Ten single H. pylori colonies were isolated per biopsy, and draft genome sequences of all isolates were obtained (Illumina MiSeq technology). Additional reference genomes were generated by Single Molecule, Real-Time (SMRT) sequencing.