title: Dynamics of bacterial communities during the ripening process of different Croatian cheese types derived from raw ewe's milk cheeses.
abstract: 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 OTU97 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.
authors.affiliation: Department Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia ; Research Unit for Environmental Genomics, Helmholtz Zentrum München, Neuherberg, Germany.
authors.forename: Mirna Mrkonjić
authors.initials: MM
authors.lastname: Fuka
authors.forename: Stefanie
authors.initials: S
authors.lastname: Wallisch
authors.forename: Marion
authors.initials: M
authors.lastname: Engel
authors.forename: Gerhard
authors.initials: G
authors.lastname: Welzl
authors.forename: Jasmina
authors.initials: J
authors.lastname: Havranek
authors.forename: Michael
authors.initials: M
authors.lastname: Schloter
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics / Q000254:growth & development*; D001483:Base Sequence; D002611:Cheese / Q000382:microbiology*; D017523:Croatia; D005260:Female; D005798:Genes, Bacterial; D006801:Humans; D064307:Microbiota / Q000235:genetics; D008892:Milk / Q000382:microbiology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012150:Polymorphism, Restriction Fragment Length / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D012756:Sheep
chemical_list: D012336:RNA, Ribosomal, 16S