title: The GyrA encoded gene: A pertinent marker for the phylogenetic revision of Helicobacter genus.
abstract: Phylogeny of Epsilonproteobacteria is based on sequencing of the 16S rRNA gene. However, this gene is not sufficiently discriminatory in Helicobacter species and alternative markers would be useful. In this study, the 16S rRNA, gyrA, hsp60, gyrB, and ureA-ureB gene sequences, as well as GyrA, HSP60 and GyrB protein sequences were analyzed as tools to support Helicobacter species phylogeny: 72 Helicobacter strains, belonging to 41 species of which 36 are validated species, were included. Results of the phylogenetic reconstructions of the GyrA gene encoded protein (approximately 730 residues) indicated the most stable trees to bootstrap resampling with a good separation of Helicobacter taxa, especially between gastric and enterohepatic species. Moreover, the GyrA tree revealed high similarity with that of the gyrB and ureA-ureB genes (restricted to urease-positive Helicobacter species). However, some differences in clustering were observed when compared to the hsp60 and 23S rRNA gene trees. Altogether, these revised phylogenies (except the 16S rRNA gene for enterohepatic Helicobacters) enabled reliable clustering of Helicobacter cinaedi and 'Flexispira' strains, determined a reliable position for Helicobacter mustelae (except the hsp60 gene) and for novel Helicobacter species proposed such as 'Helicobacter sanguini', 'Helicobacter apodemus' or 'Helicobacter winghamensis', and suggest that Helicobacter species MIT 09-6949 and MIT 05-5293 isolated from rodents constitute novel species. Although they are not commonly used to study the phylogeny of Epsilonproteobacteria, protein sequences and, in particular, the GyrA protein sequence may constitute pertinent phylogenetic markers for Helicobacter genus.
authors.affiliation: Université de Bordeaux, Laboratoire de Bactériologie, Centre National de Référence des Helicobacters et Campylobacters, F33076 Bordeaux, France(1); INSERM U853, F33076 Bordeaux, France. Electronic address: armelle.menard@u-bordeaux.fr.
authors.forename: Armelle
authors.initials: A
authors.lastname: Ménard
authors.affiliation: Université de Bordeaux, Laboratoire de Bactériologie, Centre National de Référence des Helicobacters et Campylobacters, F33076 Bordeaux, France(1); INSERM U853, F33076 Bordeaux, France.
authors.forename: Alice
authors.initials: A
authors.lastname: Buissonnière
authors.affiliation: Université de Bordeaux, Laboratoire de Bactériologie, Centre National de Référence des Helicobacters et Campylobacters, F33076 Bordeaux, France(1).
authors.forename: Valérie
authors.initials: V
authors.lastname: Prouzet-Mauléon
authors.affiliation: Université de Bordeaux, Laboratoire de Bactériologie, Centre National de Référence des Helicobacters et Campylobacters, F33076 Bordeaux, France(1); INSERM U853, F33076 Bordeaux, France.
authors.forename: Elodie
authors.initials: E
authors.lastname: Sifré
authors.affiliation: Université de Bordeaux, Laboratoire de Bactériologie, Centre National de Référence des Helicobacters et Campylobacters, F33076 Bordeaux, France(1); INSERM U853, F33076 Bordeaux, France.
authors.forename: Francis
authors.initials: F
authors.lastname: Mégraud
mesh_terms: D000818:Animals; D058893:DNA Barcoding, Taxonomic; D027081:DNA Gyrase / Q000235:genetics*; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D005819:Genetic Markers; D016998:Helicobacter / Q000145:classification* / Q000235:genetics*; D016481:Helicobacter Infections / Q000662:veterinary; D010802:Phylogeny; D016133:Polymerase Chain Reaction
chemical_list: D005819:Genetic Markers; D027081:DNA Gyrase
keywords: Chaperonin; Gyrase; Helicobacter; Phylogeny; Ribosomal gene; Taxonomy