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Characterization of the Microbiome Present in Established Biofilms Collected from Dairy Environments
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Abstract
Introduction: The presence of foodborne pathogens in food industry is often associated with the formation of biofilms. The microbiota present in these biofilms may determine the fate of the pathogens as a result of symbiotic but also antagonistic interactions.
Purpose: This study aimed to characterize the microbiome of the dairy environments where established biofilms could be found.
Methods: Fifty-four environmental samples were collected in two artisanal dairies, characterized by the production of a raw cow’s milk cheese, using scrapers and swabs focusing on previously hygienized surfaces and covering approximately 400 cm2 each. Biofilm disruption was promoted using cation exchange resin during a high-speed shaking. The samples were then centrifuged and the supernatant filter sterilized. The DNA in the cell pellets was extracted and used for enumeration of the bacterial load by qPCR. The DNA was also used for analyzing the microbiome using a 16S rRNA gene ampliconsequencing approach followed by further bioinformatic downstream analysis. Biofilm detection was based on presence of at least 2 of the 3 main matrixcomponents: Proteins, detected by precipitation, followed by SDS-PAGE and silver staining. Exopolysaccharides using a phenol-sulfuric acid method. eDNA, detection made by spectrophotometry after precipitation.
Results: Overall, 23 samples were found to have a bacterial load of >1 BCE/cm2. The remaining 31 samples had <1 BCE/cm2. In these 23 samples it was possible to detect the three matrix components in 11, only 2 components in other 11 and for one sample only 1 matrix component was detected. When analyzed the microbiome of the samples, the most prevalent genera detected were Staphylococcus, Psychrobacter, Brevidobacterium, Halomonas and Corynebacterium. Among the environments sampled, the ones associated with ventilation systems showed high microbial diversity.
Significance: This study highlights the importance of knowing the composition of the microbiota in dairy facilities as it contributes to clarify the types of
niches available for foodborne pathogens.