Stability and functional redundancy of a microbial cheese ecosystem subjected to a biotic perturbation

The cheese microbial community is dense with relatively low complexity and composed of cultivable prokaryotic and eukaryotic microorganisms. The ripening process can thus be reproduced under controlled conditions. A reduced microbial community composed of yeasts and bacteria was assembled to mimic that of smear-ripened cheese. The genomes of the microorganisms have been sequenced and annotated, which allows access to gene expression under various conditions at different ripening times. Through the use of a combined approach using omics (e.g. metatranscriptomics, volatilomics), and biochemical/microbial analyses, we have investigated the effect of a biotic perturbation, omission of some yeast, on the stability and functionality of the microbial cheese community throughout ripening. Differential analyses of metatranscriptomic data showed the resilience of the community' functions when submitted to disturbance. Multivariate integrative analysis of metatranscriptomic data and volatile compounds data resulted in the identification of key metabolic pathways correlated to the production of volatile compounds.