Phylogenetic characterization of Bifidobacterium kimbladii sp. nov., a novel species from the honey stomach of the honeybee Apis mellifera.

Six novel Bifidobacterium strains H1HS16N, Bin2N, Hma3N, H6bp22N, H1HS10N, and H6bp9N, were isolated from the honey stomach of Apis mellifera. Cells are Gram-positive, non-motile, non-sporulating, facultatively anaerobic, and fructose 6-phosphate phosphoketolase-positive. Optimal growth conditions occur at 37 °C in anaerobiosis in MRS medium added with 2 % fructose and 0.1 % L-cysteine. The 16S rRNA gene sequences analysis revealed clustering with Bifidobacterium species found in honeybees. Strains Hma3N, H6bp22N, and H1HS16N showed significant similarity to Bifidobacterium polysaccharolyticum JCM 34588, with an average similarity of 99.63 %. In contrast, strains Bin2N, H1HS10N, and H6bp9N were closely related to Bifidobacterium apousia JCM 34587, with an average similarity of 99.22 %. Moreover, strains Hma3N and H6bp22N exhibited ANI values of 96.65 % and 96.53 % when compared to Bifidobacterium polysaccharolyticum JCM 34588, while strains H1HS16N, Bin2N, H6bp9N, and H1HS10N revealed ANI values of 94.18 %, 94.33 %, 94.22 %, and 95.50 % respectively when compared to B. apousia JCM 34587. dDDH analysis confirmed that strains Hma3N and H6bp22N belong to B. polysaccharolyticum, whereas strains H1HS16N, Bin2N, H6bp9N, and H1HS10N represent a novel species. The peptidoglycan of the novel species is of the A4α type (L-Lys-D-Asp). The main cellular fatty acids of the type strain H1HS16N are C, C, C cyclo ω9c, and C ω9c. The DNA G + C content of the type strain is 60.8 mol%. Genome analyses of the strains were also conducted to determine their biosynthesis-related gene clusters, probiotic features, and ecological distribution patterns. Phenotypic and genotypic characterization show that strain H1HS16N is distinct from the type strains of other recognized Bifidobacterium species. Thus, Bifidobacterium kimbladii sp. nov. (H1HS16N = DSM 115187 = CCUG 76695) is proposed as a novel Bifidobacterium species.