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Microbial communities play an important role in cheese ripening and determine the flavor and taste of different cheese types to a large extent. However, under adverse conditions human pathogens may colonize cheese samples during ripening and may thus cause severe outbreaks of diarrhoea and other diseases. Therefore in the present study we investigated the bacterial community structure of three raw ewe's milk cheese types, which are produced without the application of starter cultures during ripening from two production sites based on fingerprinting in combination with next generation sequencing of 16S rRNA gene amplicons. Overall a surprisingly high diversity was found in the analyzed samples and overall up to 213 OTU 97  could be assigned. 20 of the major OTUs were present in all samples and include mostly lactic acid bacteria (LAB), mainly  Lactococcus , and  Enterococcus  species. Abundance and diversity of these genera differed to a large extent between the 3 investigated cheese types and in response to the ripening process. Also a large number of non LAB genera could be identified based on phylogenetic alignments including mainly  Enterobacteriaceae  and  Staphylococcacae . Some species belonging to these two families could be clearly assigned to species which are known as potential human pathogens like  Staphylococcus saprophyticus  or  Salmonella  spp. However, during cheese ripening their abundance was reduced. The bacterial genera, namely  Lactobacillus ,  Streptococcus, Leuconostoc ,  Bifidobacterium ,  Brevibacterium ,  Corynebacterium, Clostridium, Staphylococcus, Thermoanerobacterium, E. coli, Hafnia, Pseudomonas, Janthinobacterium, Petrotoga, Kosmotoga, Megasphaera, Macrococcus, Mannheimia ,  Aerococcus, Vagococcus, Weissella  and  Pediococcus  were identified at a relative low level and only in selected samples. Overall the microbial composition of the used milk and the management of the production units determined the bacterial community composition for all cheese types to a large extend, also at the late time points of cheese ripening.

Dynamics of Bacterial Communities during the Ripening Process of Different Croatian Cheese Types Derived from Raw Ewe's Milk Cheeses