Integration of multiomic data to characterize the influence of milk fat composition on Cantal-type cheese microbiota

A previous study identified differences in rind aspect between Cantal-type cheeses man- ufactured from the same skimmed milk, supplemented with cream derived either from pasture- raised cows (P) or from cows fed with maize silage (M). Using an integrated analysis of multiomic data, the present study aimed at investigating potential correlations between cream origin and met- agenomic, lipidomic and volatolomic profiles of these Cantal cheeses. Fungal and bacterial commu- nities of cheese cores and rinds were characterized using DNA metabarcoding at different ripening times. Lipidome and volatolome at the end of ripening were obtained from the previous study. Rind microbial communities, especially fungal communities, were influenced by cream origin. Among bacteria, Brachybacterium were more abundant in P-derived cheeses than in M-derived cheeses after 90 and 150 days of ripening. Sporendonema casei, a yeast added as ripening starter during Cantal manufacture and which contributes to rind typical aspect, had a lower relative abundance in P- derived cheeses after 150 days of ripening. Relative abundance of this fungus was highly negatively correlated to concentrations of C18 polyunsaturated fatty acids and to concentrations of particular volatile organic compounds, including 1-pentanol and 3-methyl-2-pentanol. Overall, these results question the match between primary production conditions, expected cheese appearance and used starters.