Relative abundance of genetic lineages during cheese manufacturing as determined by AFLP typing of randomly picked isolates plated on complementary media. Community dynamics has an effect on the functionality during cheese manufacturing. The key flavor compounds in Gouda are the metabolic side products of glycolysis (mostly lactose and citrated derived), lipolysis and amino-acid metabolism. Therefore, the better survival of citrate utilizing L. lactis subsp. lactis biovar diacetylactis and Lc. mesenteroides populations (genetic lineage 2 and 4 and 8) after brining is expected to enhance the flavor formation via citrate metabolism. Amino-acid-derived flavor development, on the other hand, is enhanced with the concerted activity of intact and lysed cells, and the intracellular peptidase complement of lysed L. cremoris strains after brining may control the free amino-acid pool during ripening.