Cheese microbiome profiling : a metaproteomic approach

Italian typical products sold all over the world are hard cheeses such as Grana Padano PDO. The changes, which more frequently affects the dairy production of hard cheeses is known as late blowing. The main “etiological” agents responsible for this alteration are the clostridia. The butyric fermentation, particularly marked in the fermentation process of Grana Padano PDO, is currently being challenged by the addition of lysozyme. Lysozyme, a natural antibiotic, causes an inhibition of the growth of clostridia minimizing the butyric fermentation. The overall goal of primary interest to this project is to develop and increase the knowledge of the main microbiological factors that influence the late blowing and then to reduce the late blowing without the use of lysozyme by using the molecular interactions of microbial consortia to fight clostridia. For this scope we used combined metaproteomic approach for the identification of the protein patterns of microbial origin related with the process of butyric fermentation. Samples involved for this study was 12 months-old, were first depleted by caseins, tripsinized and analyzed by different shotgun approaches. Using an hybrid bioinformatic pipeline we obtained a metaproteomic profile from each sample. We highlighted the relative composition of microflora during maturation, with or without add of antibacterial factor and with blowing defects or not. To investigate metabolic changes linked to cheese maturation and preparation the bacterial proteins detected in each sample were functional classified using SEED and KEGG . We show for the first time the characteristic microbiome from each Grana Padano ripening condition. Acknowledgements Work supported by FILIGRANA project, financed from MiPAAF D.M 25741/7303/11 - 01/12/2011 References: 1. Mitra, S., et al., Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. BMC Bioinformatics, 2011. 12 Suppl 1: p. S21.