Helicobacter kumamotonensis sp. nov., isolated from human clinical specimens

Int J Syst Evol Microbiol. 2023 Mar;73(3). doi: 10.1099/ijsem.0.005732.


A Gram-stain-negative, spiral bacterium (PAGU 1991T) was isolated from the blood of a patient with diffuse large B-cell lymphoma. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate was very closely related to Helicobacter equorum LMG 23362T (99.1 % similarity), originally isolated from a faecal sample from a healthy horse. PAGU 1991T was also very closely related to PAGU 1750 in our strain library (=CCUG 41437) with 99.7 % similarity. Additional phylogenetic analyses based on the 23S rRNA gene sequence and GyrA amino acid sequence further supported the close relationship between the two human isolates (PAGU 1991T and PAGU 1750) and the horse strain. However, a phylogenetic analysis based on 16S rRNA showed that the two human isolates formed a lineage that was distinct from the horse strain (less than 99.2 % similarity). In silico whole-genome comparisons based on digital DNA-DNA hybridization, average nucleotide identity based on blast and orthologous average nucleotide identity using usearch between the two human isolates and the type strain of H. equorum showed values of less than 52.40, 93.47, and 93.50 %, respectively, whereas those between the two human isolates were 75.8, 97.2, and 97.2 %, respectively. These data clearly demonstrated that the two human isolates formed a single species, distinct from H. equorum. Morphologically, the human isolates could be distinguished by the type of flagella; the human isolates showed a bipolar sheathed flagellum, whereas that of H. equorum was monopolar. Biochemically, the human isolate was characterized by growth at 42 °C under microaerobic conditions and nitrate reduction unability. We conclude that the two human isolates, obtained from geographically and temporally distinct sources, were a novel species, for which we propose the name Helicobacter kumamotonensis sp. nov., with the type strain PAGU 1991T (=GTC 16810T=CCUG 75774T).

Keywords: DNA gyrase subunit A; Helicobacter equorum; Helicobacter kumamotonensis; diffuse large B-cell lymphoma; digital DNA–DNA hybridization; enterohepatic Helicobacter.

MeSH terms

  • Animals
  • Bacterial Typing Techniques
  • Base Composition
  • DNA, Bacterial / genetics
  • Fatty Acids* / chemistry
  • Helicobacter*
  • Horses
  • Humans
  • Nucleic Acid Hybridization
  • Phylogeny
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA


  • RNA, Ribosomal, 16S
  • Fatty Acids
  • DNA, Bacterial