Characterization of the bacterial biodiversity in Pico cheese (an artisanal Azorean food)

Abstract

This work presents the first study on the bacterial communities in Pico cheese, a traditional cheese of the Azores (Portugal), made from raw cow's milk. Pyrosequencing of tagged amplicons of the V3-V4 regions of the 16S rDNA and Operational Taxonomic Unit-based (OTU-based) analysis were applied to obtain an overall idea of the microbiota in Pico cheese and to elucidate possible differences between cheese-makers (A, B and C) and maturation times.Pyrosequencing revealed a high bacterial diversity in Pico cheese. Four phyla (Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes) and 54 genera were identified. The predominant genus was Lactococcus (77% of the sequences). Sequences belonging to major cheese-borne pathogens were not found. Staphylococcus accounted for 0.5% of the sequences. Significant differences in bacterial community composition were observed between cheese-maker B and the other two units that participated in the study. However, OTU analysis identified a set of taxa (Lactococcus, Streptococcus, Acinetobacter, Enterococcus, Lactobacillus, Staphylococcus, Rothia, Pantoea and unclassified genera belonging to the Enterobacteriaceae family) that would represent the core components of artisanal Pico cheese microbiota. A diverse bacterial community was present at early maturation, with an increase in the number of phylotypes up to 2 weeks, followed by a decrease at the end of ripening. The most remarkable trend in abundance patterns throughout ripening was an increase in the number of sequences belonging to the Lactobacillus genus, with a concomitant decrease in Acinetobacter, and Stenotrophomonas. Microbial rank abundance curves showed that Pico cheese's bacterial communities are characterized by a few dominant taxa and many low-abundance, highly diverse taxa that integrate the socalled "rare biosphere".2

Inhibition of bacterial growth in sweet cheese whey by carbon dioxide as determined by culture-independent community profiling

“…This can be achieved by culture-independent community profiling using next generation sequencing of barcoded 16S rRNA gene amplicons (Degnan and Ochman, 2012;Rothberg and Leamon, 2008). Pyrosequencing has been used in a large number of recent studies in which the microbial communities of dairy products were characterised, including raw and pasteurised milk and various types of cheese (Aldrete-Tapia et al, 2014;de Filippis et al, 2014;de Pasquale et al, 2014;Ercolini et al, 2012;Guidone et al, 2016;Masoud et al, 2011;Masoud et al, 2012;Quigley, McCarthy, et al, 2013;Riquelme et al, 2015). Many of the cheese studies cover various stages of cheese making, and fermented whey used as natural whey culture has been analysed (Aldrete-Tapia et al, 2014).…”

The use of 16S rRNA gene metagenetic monitoring of refrigerated food products for understanding the kinetics of microbial subpopulations at different storage temperatures: the example of white pudding

“…Fortunately, molecular technologies can elucidate the microbial communities, including the identification and quantification of culturable and non-culturable organisms, and can do so at a much higher resolution than was previously possible with culture-based methods (Kergourlay et al, 2015;Elizaquível et al, 2015). Many bacterial species putatively responsible for food spoilage have been reported, thanks to the development of high throughput sequencing methods, that allow for a more detailed and deeper description of bacterial species present in food (Benson et al, 2014;Chaillou et al, 2014;Delcenserie et al, 2014;Galimberti et al, 2015;Riquelme et al, 2015). These works are mainly limited to the description of the product's microbiota during its shelf life.…”

Emerging DNA-based technologies to characterize food ecosystems

“…Again, in the case of wine, the wine cellar yeasts and bacteria could actively contribute to the chemical modification of grape juice to obtain wine with specific organoleptic properties (Bokulich, Ohta, Richardson, & Mills, 2013;David et al, 2014). Environmental microorganisms represent an important source of biodiversity to differentiate a certain food product from the others, even at a reduced spatial production scale (Quigley et al, 2012;Riquelme et al, 2015). For these reasons, modern food companies should not underestimate the importance of knowing the composition of microbial community accompanying food from farms to consumer's fork or glass.…”

“…Another emblematic case is that of Pico Cheese, an artisanal dairy cattle product manufactured by few Azorean (Portugal) producers without the addition of starter cultures (Riquelme et al, 2015).…”

“…Given the ongoing loss of local producers and the necessity of preserve its peculiarity and enhance its marketability even at a semi-industrial scale production, Riquelme et al (2015) examined in depth the microbiota diversity and dynamics during ripening of Pico Cheese. Researchers characterized the core bacterial components (Lactococcus, Streptococcus and some unclassified…”