Analysis of the Bacterial Diversity of Paipa Cheese (a Traditional Raw Cow's Milk Cheese from Colombia) by High-Throughput Sequencing.

Background: Paipa cheese is a traditional, semi-ripened cheese made from raw cow's milk in Colombia. The aim of this work was to gain insights on the microbiota of Paipa cheese by using a culture-independent approach.

Method: two batches of Paipa cheese from three formal producers were sampled during ripening for 28 days. Total DNA from the cheese samples was used to obtain 16S rRNA gene sequences by using Illumina technology.

Results: was the main phylum found in the cheeses (relative abundances: 59.2-82.0%), followed by , and . was the main genus, but other lactic acid bacteria (, and ) were also detected. was also relevant in some cheese samples. The most important were , and . and (others) were detected in all cheese samples. and were detected in some samples. and were also relevant. Other minor genera detected were , 1 and . The principal coordinates analysis suggested that there were producer-dependent differences in the microbiota of Paipa cheeses.

Conclusions: lactic acid bacteria are the main bacterial group in Paipa cheeses. However, other bacterial groups, including spoilage bacteria, potentially toxin producers, and bacteria potentially pathogenic to humans and/or prone to carry antimicrobial resistance genes are also relevant in the cheeses.