Exploring the industrial potential of Lactobacillus delbrueckii subsp. bulgaricus by population genomics and genome-wide association study (GWAS) analysis

Lactobacillus delbrueckii subsp. bulgaricus (L. delbrueckii subsp. bulgaricus) is one of the most commonly used starter-cultures for yoghurt production. However, how its genetic background affects the acid production capacity is unclear. This study investigated the industrial potential of L. delbrueckii subsp. bulgaricus by population genomics and genome-wide association study (GWAS) analysis. To meet our goal, population genetics and functional genomics analyses were performed on 188 newly sequenced L. delbrueckii subsp. bulgaricus strains isolated from naturally fermented dairy products together with 19 genome sequences retrieved from the NCBI database. Four distinct clusters were identified, and they were correlated with the geographical sites where the samples were collected. The GWAS analysis about acidification fermentation result with sucrose fortified reconstituted skimmed milk revealed significant association between the L-lactate dehydrogenase (lldD; Ldb2036) and the bacterial acid production rate. Our study has broadened the understanding of the population structure and genetic diversity of L. delbrueckii subsp. bulgaricus by identifying potential targets for further research, development, and utilization of lactic acid bacteria in the dairy industry.