Genetic Characterisation of Closely Related Lactococcus lactis Strains Used in Dairy Starter Cultures

The complex microbiota of cheese starters plays a key role in determining the structure and flavour of the final product, primarily through their acid-forming capacity, protease activity, and exopolysaccharide synthesis. However, the specific microbial communities underlying the unique qualities of artisanal cheeses remain poorly understood. This study presents the microbiological and molecular genetic characterisation of the microbiome isolated from an artisanal cheese starter in Kosh-Agach, Altai, Russia. Metagenomic analysis of this starter revealed the presence of three bacterial genomes corresponding to those of <i>Lactococcus lactis</i>. Pure cultures from this starter were obtained by sequential subculture, and seventeen colonies displaying distinct characteristics on differential media were selected. Genome sequencing was performed for each colony. Bioinformatic analysis based on the <i>rpoB</i> gene grouped the isolates into three clusters, each corresponding to a distinct strain of <i>Lactococcus lactis</i> subsp. <i>diacetilactis</i>. This classification was further confirmed by microbiological and microscopic analyses. A notable finding was that none of the strains produced the characteristic aroma compounds of <i>L. l.</i> subsp. <i>diacetilactis</i>, namely, diacetyl and CO₂. The functional properties and metabolic characteristics of this starter consortium are discussed.