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

Abstract

As part of a larger study on Epsilonproteobacteria carried by wild birds in the city of Valdivia (southern Chile), two curved rod-shaped Gram-stain-negative strains (A82T and WB-40) were recovered from faecal samples and subjected to a taxonomic study. Results of a genus-specific PCR showed that these isolates belonged to the genus Helicobacter. Further identification by 16S rRNA and hsp60 (60 kDa heat-shock protein) gene sequence analysis revealed that they formed a separate phylogenetic clade, different from other known Helicobacter species with ‘Helicobacter burdigaliensis’ CNRCH 2005/566HT and Helicobacter valdiviensis WBE14T being the most closely related species. This was confirmed by core-genome phylogeny as well as digital DNA–DNA hybridization and average nucleotide identity analyses between the genomes of strains A82T and WB-40 and all other Helicobacter species. The draft genome sequences of A82T and WB-40, obtained by Illumina NextSeq 2000 sequencing, consisted of 1.6 Mb with a G+C content of 31.9–32.0 mol%. The results obtained from the phylogenetic and genomic characteri-zation, together with their different morphological and biochemical features, revealed that these two strains represent a novel species, for which we propose the name Helicobacter ibis sp. nov. with A82T (=LMG 32718T=CCCT 22.04T) as the type strain.