Philodulcilactobacillus myokoensis gen. nov., sp. nov., a fructophilic, acidophilic, and agar-phobic lactic acid bacterium isolated from fermented vegetable extracts

Lactic acid bacteria are commonly in the fermentation industry and pose potential positive effects on health. In this study, a new lactic acid bacterium was isolated from fermented vegetable extracts in Myoko, Niigata, Japan. This bacterium is fructophilic, acidophilic, and hard to grow on agar medium. The isolate is Gram-stain-positive, non-spore-forming, non-motile, rod-shaped, and catalase-negative. Growth occurred at pH 3.5–5.5, with optimal growth at pH 4.5–5.0. The cells formed colonies on a solid MRS medium with 20% (w/v) sucrose and 0.8% (w/v) gellan gum under anaerobic conditions. The bacterium was able to grow on up to 50% (w/v) sucrose but not on d-glucose. Moreover, 16S rRNA gene sequence analysis revealed that the strain was most closely related to Apilactobacillus ozensis (93.1% sequence similarity). The values of average nucleotide identity, digital DNA-DNA hybridization, average amino acid sequence identity, and amino acid identity of conserved genes were calculated between the isolated strain (type strain is WR16-4(T) = NBRC 115064(T) = DSM 112857(T)) and its phylogenetically closest type strains. The average nucleotide identity values (73.36–78.28%) and DNA-DNA hybridization values (16.3–32.9%) were significantly lower than the threshold values for species boundaries. The average amino acid sequence identity values (53.96–60.88%) were significantly below the threshold boundary of genus demarcation (68%). The amino acid identity of conserved genes values compared to strain WR16-4(T) were the genera Apilactobacillus, Nicoliella spurrieriana SGEP1_A5(T), Acetilactobacillus jinshanensis HSLZ-75(T), and Fructilactobacillus were 62.51–63.79%, 62.87%, 62.03%, and 58.00–61.04%, respectively. The 16S rRNA gene and core genome phylogenetic trees suggested that this novel strain was most closely related to the type strain of A. jinshanensis HSLZ-75(T). Based on the physiological, morphological, and phenotypical characteristics of strain WR16-4(T), we propose its classification as a novel genus, Philodulcilactobacillus myokoensis gen. nov., sp. nov.