Lactococcus lactis Diversity Revealed by Targeted Amplicon Sequencing of purR Gene, Metabolic Comparisons and Antimicrobial Properties in an Undefined Mixed Starter Culture Used for Soft-Cheese Manufacture

Abstract

The undefined mixed starter culture (UMSC) is used in the manufacture of cheeses. Deciphering UMSC microbial diversity is important to optimize industrial processes. The UMSC was studied using culture-dependent and culture-independent based methods. MALDI-TOF MS enabled identification of species primarily from the Lactococcus genus. Comparisons of carbohydrate metabolism profiles allowed to discriminate five phenotypes of Lactococcus (n = 26/1616). The 16S sequences analysis (V1–V3, V3–V4 regions) clustered the UMSC microbial diversity into two Lactococcus operational taxonomic units (OTUs). These clustering results were improved with the DADA2 algorithm on the housekeeping purR sequences. Five L. lactis variants were detected among the UMSC. The whole-genome sequencing of six isolates allowed for the identification of the lactis subspecies using Illumina® (n = 5) and Pacbio® (n = 1) technologies. Kegg analysis confirmed the L. lactis species-specific niche adaptations and highlighted a progressive gene pseudogenization. Then, agar spot tests and agar well diffusion assays were used to assess UMSC antimicrobial activities. Of note, isolate supernatants (n = 34/1616) were shown to inhibit the growth of Salmonella ser. Typhimurium CIP 104115, Lactobacillus sakei CIP 104494, Staphylococcus aureus DSMZ 13661, Enterococcus faecalis CIP103015 and Listeria innocua CIP 80.11. Collectively, these results provide insightful information about UMSC L. lactis diversity and revealed a potential application as a bio-protective starter culture.

Bacteriocin Production by <i>Lactobacilli</i> and Their Role as Antibacterial Tool against Common Pathogens

“…These pathogens were found to be sensitive to bacteriocin 17) . Curvacin A encoding gene was identified in both the Lactobacillus curvatus and Lactobacillus sake 18) . In this study both strain M3 (Lactococcus garvieae) and M11 (Lactobacillus curvatus) were amplified with curvacin gene.…”

Universal drivers of cheese microbiomes

“…Among the studies which did report on starter culture use, 13.3% did not use any starter culture, while 20.8%, 12.5%, and 1.7% focused on cheeses made with commercial, local, and unspecified starter cultures, respectively ( Figure 3 C). Only 2.5% of the studies 2 , 19 , 21 sequenced the starter cultures used in the production of the cheeses using 16S rRNA gene amplicon sequencing ( Table S1 ). Physicochemical parameters were reported for the minority of studies: on average, salinity was 2.5 ± 1.1% (reported for 11% of the studies), pH was 5.3 ± 0.5 (reported for 18% of studies), and cheeses were ripened at 10.7 ± 5.5°C (reported for 26% of the studies, Figure 4 ).…”

Bacteriocin-mediated inhibition of some common pathogens by wild and mutant Lactobacillus species and in vitro amplification of bacteriocin encoding genes

“…Generally, one species of bacteria may produce more than one type of bacteriocin and one bacteriocin may not produce by single species of bacteria. Two subspecies of L. plantarum isolated from different sources, such as fermented sausages and cucumber fermentation were shown to have the same plantaricin encoding gene PlnA [ 22 , 23 ]. Curvacin A encoding gene was identified in both the L. curvatus and Lactobacillus sakeii [ 24 ].…”