Bifidobacterium tibiigranuli sp. nov. isolated from homemade water kefir

Int J Syst Evol Microbiol. 2020 Mar;70(3):1562-1570. doi: 10.1099/ijsem.0.003936.

Abstract

Two Bifidobacterium strains, TMW 2.2057T and TMW 2.1764 were isolated from two different homemade water kefirs from Germany. Both strains were oxidase- and catalase-negative and Gram-staining-positive. Cells were non-motile, irregular rods that were aerotolerant anaerobes. On basis of fructose 6-phosphate phosphoketolase activity, they were assigned to the family Bifidobacteriaceae. Comparative analysis of 16S rRNA and concatenated housekeeping genes (clpC, dnaB, dnaG, dnaJ, hsp60 and rpoB) demonstrated that both strains represented a member of the genus Bifidobacterium, with Bifidobacterium subtile DSM 20096T as the closest phylogenetic relative (98.35 % identity). Both strains can be distinguished using randomly amplified polymorphic DNA fingerprinting. Analysis of concatenated marker gene sequences as well as average nucleotide identity by blast (ANIb) and in silico DNA-DNA hybridization (isDDH) calculations of their genome sequences confirmed Bifidobacterium subtile DSM 20096T as the closest relative (87.91 and 35.80 % respectively). All phylogenetic analyses allow differentiation of strains TMW 2.2057T and TMW 2.1764 from all hitherto described species of the genus Bifidobacterium with validly published names. We therefore propose a novel species with the name Bifidobacterium tibiigranuli, for which TMW 2.2057T (=DSM 108414T=LMG 31086T) is the type strain.

Keywords: Bifidobacterium; Bifidobacterium tibiigranuli; New species; water kefir.

MeSH terms

  • Bacterial Typing Techniques
  • Base Composition
  • Bifidobacterium / classification*
  • Bifidobacterium / isolation & purification
  • DNA, Bacterial / genetics
  • Fatty Acids / chemistry
  • Feces / microbiology
  • Food Microbiology*
  • Genes, Bacterial
  • Germany
  • Kefir / microbiology*
  • Nucleic Acid Hybridization
  • Phylogeny*
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA

Substances

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