Subspecies Classification and Comparative Genomic Analysis of HL1 and M1 for Potential Niche-Specific Genes and Pathways.

(1) Background: Strains HL1 and M1, isolated from kefir grains, have been tentatively identified, based on their partial 16S rRNA gene sequences, as . The two strains demonstrated different health benefits. Therefore, not only the genetic factors exerting diverse functionalities in different strains, but also the potential niche-specific genes and pathways among the strains, should be identified. (2) Methods: Phenotypic and genotypic approaches were employed to identify strains HL1 and M1 at the subspecies level. For the further characterization of the probiotic properties of both strains, comparative genomic analyses were used. (3) Results: Both strains were identified as subsp. . According to the COG function category, dTDP-rhamnose and rhamnose-containing glycans were specifically detected in the subsp. genomes. Three unique genes (, , and ) encoding glycosyltransferase in the EPS gene cluster, and the ImpB/MucB/SamB family protein encoding gene were found in HL1 and M1. The specific ability to degrade arginine via the ADI pathway was found in HL1. The presence of the complete glycogen metabolism () operon in the strains suggested the importance of glycogen synthesis to enable colonization in kefir grains and extend survival under environmental stresses. (4) Conclusions: The obtained novel information on the potential genes and pathways for polysaccharide synthesis and other functionalities in our HL1 and M1 strains could be applied for further functionality predictions for potential probiotic screening.