Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese

This study showed how new molecular methods, 16S rRNA gene marker sequencing, propidium monoazide treatment of bacteria cells and metagenomics, can be applied to investigate cheese microbiota composition and metabolism during ripening in Dutch-type cheeses manufactured with different processes. While whey dilution did not have any effect on the microbiota composition, scalding temperature was shown to influence the microbial dynamics during ripening. A higher abundance of Leuconostoc spp. and Lactobacillus spp. was detected during ripening under all cheese making conditions considered, most probably caused by an increase in Lactococcus cell lysis during ripening. The metagenomic approach determined that the microbiota metagenomes contained a high number of genes involved in the carbohydrate metabolism and, during ripening, an increased number of metabolic functions, such as carbohydrate and protein metabolism, was detected. This can be attributed to the growth of minor groups of bacteria present in the starter (Leuconostoc) and non-starter microbiota.