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 H02T with 97.0–97.1 % identity levels and they formed a novel phylogenetic line within the genus Helicobacter . Faydin-H64 and Faydin-H70T 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-H70T were 35.3 mol% and 1.7 Mb, respectively. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain Faydin-H70T and its close phylogenetic neighbour H. winghamensis ATCC BAA-430T were determined as 81.7 and 34.9 %, respectively. Pairwise sequence comparison showed that it was closely related to H. ganmani CMRI H02T however it shared the highest ANI and dDDH values with H. winghamensis ATCC BAA-430T. 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 112556T=LMG 32335T).

Helicobacter ibis sp. nov., isolated from faecal droppings of black-faced ibis (Theristicus melanopis)

“…Finally, along with several known Campylobacter and Helicobacter species, three isolates suspected of belonging to a new Helicobacter species were obtained from the 270 wild bird faecal droppings analysed. These isolates were genotyped by enterobacterial repetitive intergenic consensus PCR [11], resulting in two strains with different genotypes (A82 T isolated on CBA and mCCDA, and WB-40 isolated only on CBA; data not shown). In an attempt to identify the origin of the samples, faecal DNA was extracted using the stool DNA kit (Omega Biotek) and the mitochondrial COI (cytochrome c oxidase subunit 1) gene was amplified and sequenced using the universal primers BirdF1 and BirdR1, and alternative reverse primer BirdR2 [12].…”

“…‡The tests were assessed in plates with 32 mg L -1 of the respective antibiotic. [37]; Eaton et al [39]); 3, H. pullorum (Stanley et al [40]); 4, H. rodentium (Shen et al [41]); 5, H. mesocricetorum (Simmons et al [42]); 6, H. ganmani (Robertson et al [43]); 7, H. canadensis (Fox et al [8]); 8, H. valdiviensis (Collado et al [6]); 9, H. monodelphidis (Shen et al [44]); 10, H. turcicus (Aydin et al [11]); 11, H. colisuis (Gruntar et al [45]). +, 100 % of strains positive; -, 100 % of strain negative; (+), 70-94 % of strains positive; (-), 7-33 % of strains positive; ±, 42-66 % of strains positive; W, weak growth; S, sensitive; R, resistant; V, variable; ND, not determined; M, monopolar; B, bipolar.…”