Comparison of Genomes, Resistomes, and Antimicrobial Properties of the Three Lactococcus lactis Strains from Fermented Milk and Cereal Products of South Africa and Russia

Abstract Whole-genome sequencing was carried out, and the main characteristics of the genomes of three new strains of L. lactis AM1, MA1, and dlA, isolated from fermented milk and cereal grain products of South Africa and Russia, were established. The dual approach of in vitro and in silico analysis used in this work allowed us to assess more fully the bacteriocinogenic potential and antibiotic resistance of L. lactis strains. It was shown that L. lactis AM1 and dlA had an antagonistic effect against the test cultures of Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 6538. The growth retardation of E. coli and S. aureus after 48 hours of cocultivation was 65–75 and 30–50%, respectively. The L. lactis MA1 strain did not exhibit a significant antagonistic effect; the growth inhibition of E. coli and S. aureus was 13 and 26%, respectively. According to the results of in silico analysis using the BAGELv4.0 service, gene clusters of class IId lactococcin-like bacteriocins were found in the genomes of all three strains. In the genomes of the dlA and AM1 strains, the sactipeptide cluster, a class I bacteriocin, is additionally annotated. In silico analysis of the L. lactis genomes showed the absence of transmissible antibiotic resistance genes, and all three strains showed a phenotype susceptible to the main classes of clinically relevant antibiotics (ampicillin, streptomycin, kanamycin, gentamicin, erythromycin, clindamycin, vancomycin, tetracycline, and chloramphenicol). Taken together, the results provide valuable information about the intraspecific diversity of L. lactis and indicate the promise of using new strains as starter cultures and biopreservatives.