Helicobacter turcicus sp. nov., a catalase- negative new member of the helicobacter genus, isolated from anatolian ground squirrel (spermophilus xanthoprymnus) in Turkey

Abstract

Eleven Gram-negative, curved and S-shaped, oxidase activity positive, catalase activity negative bacterial isolates recovered from faeces of Anatolian ground squirrel (Spermophilus xanthoprymnus) in the city of Kayseri, Turkey, were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR revealed that these isolates belonged to the genus Helicobacter. The 16S rRNA gene sequence analysis revealed that the 11 isolates had over 99 % sequence identity with each other and were most closely related to Helicobacter ganmani CMRI H02(T) with 97.0-97.1 % identity levels and they formed a novel phylogenetic line within the genus Helicobacter. Faydin-H64 and Faydin-H70(T) strains were subjected to gyrA and atpA gene and whole genome sequence analyses. These two Helicobacter strains formed separate phylogenetic clades, divergent from other known Helicobacter species. The DNA G+C content and genome size of the strain Faydin-H70(T) were 35.3 mol% and 1.7 Mb, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain Faydin-H70(T) and its close phylogenetic neighbour H. winghamensis ATCC BAA-430(T) were determined as 81.7 and 34.9%, respectively. Pairwise sequence comparison showed that it was closely related to H. ganmani CMRI H02(T) however it shared the highest ANI and dDDH values with H. winghamensis ATCC BAA-430(T). The data obtained from the polyphasic taxonomy approach, including phenotypic characterization and whole-genome sequences, revealed that these strains represent a novel species within the genus Helicobacter, for which the name Helicobacter turcicus sp. nov., is proposed with Faydin-H70T as the type strain (=DSM 112556(T)=LMG 32335(T)).