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Int J Mol Sci. 2018 Jun 21;19(7). pii: E1831. doi: 10.3390/ijms19071831.

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

Author information

1
Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal. vale.filipa@gmail.com.
2
Laboratoire de Bacteriologie, Centre National de Référence des Campylobacters et Hélicobacters, Place Amélie Raba Léon, 33076 Bordeaux, France. f.vale@ff.ul.pt.
3
INSERM U1053-UMR Bordeaux Research in Translational Oncology, BaRITOn, 33000 Bordeaux, France. f.vale@ff.ul.pt.

Abstract

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

PMID:
29933614
PMCID:
PMC6073503
DOI:
10.3390/ijms19071831
[Indexed for MEDLINE]
Free PMC Article

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