Metatranscriptomics of semi-hard cheeses throughout making and ripening

Metatranscriptomics of a model of semi-hard cheeses to identify the succession of bacterial metabolisms leading to acidification and production of volatil aroma coumpounds throughout making and ripening. Two manufactures were performed (biological replicates) using 3 previously sequenced bacterial strains as starters to inoculate milk : Lactococcus lactis CIRM-BIA1206, Lactiplantibacillus plantarum CIRM-BIA465, Propionibacterium freudenreichii CIRM-BIA122. Cheeses were sampled at five steps : moulding, demoulding, after salting, after 4-week ripening and after 7-week ripening. RNA was extracted from bacterial cells harvested from cheese samples and Illumina paired-end sequenced. Reads were mapped on starter annotated genomes. Differentially expressed genes were identified using EdgeR. Results highlighted specific carbon metabolism and successive inductions of aroma coumpounds pathways.