Streptococcus raffinosi sp. nov., isolated from human breast milk samples

Novel Gram-positive, catalase-negative, α-haemolytic cocci were isolated from breast milk samples of healthy mothers living in Hanoi, Vietnam. The 16S rRNA gene sequences of these strains varied by 0-2 nucleotide polymorphisms. The 16S rRNA gene sequence of one strain, designated as BME SL 6.1^T, showed the highest similarity to those of Streptococcus salivarius NCTC 8618^T (99.4 %), Streptococcus vestibularis ATCC 49124^T (99.4 %), and Streptococcus thermophilus ATCC 19258^T (99.3 %) in the salivarius group. Whole genome sequencing was performed on three selected strains. Phylogeny based on 631 core genes clustered the three strains into the salivarius group, and the strains were clearly distinct from the other species in this group. The average nucleotide identity (ANI) value of strain BME SL 6.1^T exhibited the highest identity with S. salivarius NCTC 8618^T (88.4 %), followed by S. vestibularis ATCC 49124^T (88.3 %) and S. thermophilus ATCC 19258^T (87.4 %). The ANI and digital DNA-DNA hybridization values between strain BME SL 6.1^T and other species were below the cut-off value (95 and 70 %, respectively), indicating that it represents a novel species of the genus Streptococcus. The strains were able to produce α-galactosidase and acid from raffinose and melibiose. Therefore, we propose to assign the strains to a new species of the genus Streptococcus as Streptococcus raffinosi sp. nov. The type strain is BME SL 6.1^T (=VTCC 12812^T=NBRC 116368^T).