Relating Phage Genomes to Helicobacter pylori Population Structure: General Steps Using Whole-Genome Sequencing Data

Int J Mol Sci. 2018 Jun 21;19(7):1831. doi: 10.3390/ijms19071831.


The review uses the Helicobacter pylori, the gastric bacterium that colonizes the human stomach, to address how to obtain information from bacterial genomes about prophage biology. In a time of continuous growing number of genomes available, this review provides tools to explore genomes for prophage presence, or other mobile genetic elements and virulence factors. The review starts by covering the genetic diversity of H. pylori and then moves to the biologic basis and the bioinformatics approaches used for studding the H. pylori phage biology from their genomes and how this is related with the bacterial population structure. Aspects concerning H. pylori prophage biology, evolution and phylogeography are discussed.

Keywords: Helicobacter pylori; evolution; genome; phage; phylogeography.

Publication types

  • Historical Article
  • Review

MeSH terms

  • Africa / epidemiology
  • Asia / epidemiology
  • Bayes Theorem
  • Biological Coevolution
  • Europe / epidemiology
  • Genes, Essential
  • Genome, Bacterial*
  • Genome, Viral*
  • Helicobacter Infections / epidemiology*
  • Helicobacter Infections / microbiology
  • Helicobacter Infections / transmission
  • Helicobacter pylori / classification
  • Helicobacter pylori / genetics*
  • Helicobacter pylori / isolation & purification
  • Helicobacter pylori / virology
  • History, Ancient
  • Human Migration / history
  • Humans
  • Interspersed Repetitive Sequences
  • Phylogeny
  • Phylogeography
  • Prophages / classification
  • Prophages / genetics*
  • Prophages / isolation & purification
  • Virulence Factors / genetics*
  • Whole Genome Sequencing


  • Virulence Factors