Changes in transcription profiles reflect strain contributions to defined cultures of Lactococcus lactis subsp cremoris during milk fermentation

Cheddar cheese production uses mixed starters composed of Lactococcus lactis subsp. cremoris strains with complementary or competing enzymatic activity. However, strain interactions within the same subspecies are difficult to investigate by conventional microbiological methods. This study uses fluorescent RNA arbitrarily primed PCR (FRAP-PCR) to analyze the association of three L. lactis subsp. cremoris strains (LL074, LL225, and LL390 with proteinase types: PI, PIII, and PI/PIII, respectively) by monitoring whole transcription profiles. The effect of strain association was demonstrated by distinguishing profiles obtained with pure cultures from those obtained with defined mixed cultures. Both strains LL225 and LL390 dominated culture activity when in dual culture with strain LL074. The three-strain starter was also dominated by LL225 and LL390, in an approximately equal ratio which was stable over 35 generations. Strain LL225 had a stronger inhibitory effect on the growth of strain LL074 than LL390 did, showing incompatibility between strains LL225 and LL074. A new economic and semi-quantitative single-nucleotide polymorphism detection technique was developed and validated the results obtained by FRAP-PCR. Strain disequilibrium detected by FRAP-PCR could be related to inhibition of strain LL074 with a PI-type proteinase by the LL225 strain with a PIII-type proteinase. Strain compatibility could be characterized using these methods, leading to an improved understanding of mixed culture association of lactococcal strains.