cheese rind and curd microbiota 16S rRNA gene sequencing

The microorganisms that inhabit cheese contribute greatly to the flavor and development of the final product. While the rind and curd microbiota have been characterized separately, there is limited information on how the structure and function of microbial communities in rinds and curds vary within and amongst cheeses. To better understand the differences in community structure and function between communities of cheese rinds and curds, we combined culture-based methods with culture-independent community profiling of curds and rinds. Consistent with our hypothesis, rinds contained greater taxonomic diversity than curds. More specifically, Lactobacillales dominated curd communities while members from the order Actinomycetales were found in high abundance in rind communities. Communities also varied more between rinds and curds than among cheeses produced from different milk types. To better understand microbial community functions, we cultured and assayed isolates for antibiotic susceptibility and carbon source utilization. Among European and U.S. cheeses, 70% of all susceptible isolates were cultured from U.S. cheeses. Overall, our study explored the differences within and between rind and curd microbial communities of seven distinct natural rind cheeses, and demonstrated that at the community and isolate level the cheese microbiome was diverse and metabolically complex.