Abstract
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: Firmicutes was the main phylum found in the cheeses (relative abundances: 59.2–82.0%), followed by Proteobacteria, Actinobacteria and Bacteroidetes. Lactococcus was the main genus, but other lactic acid bacteria (Enterococcus, Leuconostoc and Streptococcus) were also detected. Stapylococcus was also relevant in some cheese samples. The most important Proteobacteria were Enterobacteriaceae, Aeromonadaceae and Moraxellaceae. Enterobacter and Enterobacteriaceae (others) were detected in all cheese samples. Serratia and Citrobacter were detected in some samples. Aeromonas and Acinetobacter were also relevant. Other minor genera detected were Marinomonas, Corynebacterium 1 and Chryseobacterium. 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.
Highlights
The analysis of microbial communities by culture-dependent methods is laborious and requires the use of selective methods and conditions that are specific for each microbial group
In the milk and dairy industry, numerous studies based on High-throughput sequencing (HTS) technologies have been carried out [3] with different purposes, e.g., to decipher the microbiota from farm environments and animals [4], raw and pasteurized milk [5], transportation tanks, vats, utensils and cheese production facilities [6,7,8] and the variations associated with season [6] or animal feeding [9], to establish relationships between microbial communities in the raw materials, the environment and the finished product [8,9,10], to study the changes in the bacterial communities associated with cheese-making [9,11] and cheese ripening processes [9,12,13,14,15], or to determine the microbial composition of cheeses and cheese varieties [16,17,18,19]
The total number of reads assigned to operational taxonomic units (OTUs) per sample ranged from 100,681 to 189,360 (Table 1)
Summary
The analysis of microbial communities by culture-dependent methods is laborious and requires the use of selective methods and conditions that are specific for each microbial group. 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. Stapylococcus was relevant in some cheese samples. Enterobacter and Enterobacteriaceae (others) were detected in all cheese samples. 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. Other bacterial groups, including spoilage bacteria, potentially toxin producers, and bacteria potentially pathogenic to humans and/or prone to carry antimicrobial resistance genes are relevant in the cheeses
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