Comparative metataxonomics based on 16S rRNA and culture-dependent analysis of two Brazilian cheese production facilities suggests a commom core microbiota

Dairy foods are complex ecosystems composed of microorganisms from different origins (milk borne, food-contact surfaces, processing environment) that can impact flavor and safety of final products. Data on the microbiota of Brazilian cheeses are scarce, especially considering the use of high throughput DNA sequencing approaches, and this paper describes a study carried out in two independent Brazilian cheese factories (A - artisanal and B - commercial), to determine the dairy-related microbiota. For this in total, 27 samples (from food, equipment and environment) were collected in one artisanal and one commercial dairy plant, for analyses by culture-dependent method combined with metataxonomics. Metagenomic DNA was extracted from samples with a commercial kit and metataxonomics based on 16S rRNA was done with the DNA sequencer MiSeq (Illumina®), followed by bioinformatics. Overall, the results indicated there is a core bacterial microbiota for Brazilian cheeses but there are also unique microorganisms, depending on the processing site. This may be important to further evaluate the microbial species and metabolites typical in Brazilian cheeses.