Microbial profiles of Greek PDO cheeses assessed with amplicon metabarcoding

Michailidou, Sofia; Pavlou, Eleftherios; Pasentsis, Konstantinos; Rhoades, Jonathan; Likotrafiti, Eleni; Argiriou, Anagnostis

doi:10.1016/j.fm.2021.103836

Cited by 24 publications

(34 citation statements)

References 45 publications

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“…The Gram-positive species belonging to the phylum of Firmicutes, especially lactococci, lactobacilli and streptococci, were dominant in the microbiota of all the samples (Figure 1a). These results are consistent with the findings of similar studies that have revealed the prevalence of Firmicutes and, in particular, of the Lactococcus, Lactobacillus and Streptococcus genera in goat and sheep milk and cheese [27][28][29][30][31]. The second most abundant phylum was Proteobacteria, which is one of the most diverse phyla of Gram-negative bacteria with many known human pathogens and in which the various species of Enterobacteriaceae prevailed, followed by Moraxellaceae (Figure 1b).…”

Section: Bacterial Diversity Of Feta Cheesesupporting

confidence: 91%

Characterization of Bacterial Microbiota of P.D.O. Feta Cheese by 16S Metagenomic Analysis

et al. 2021

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Background: The identification of bacterial species in fermented PDO (protected designation of origin) cheese is important since they contribute significantly to the final organoleptic properties, the ripening process, the shelf life, the safety and the overall quality of cheese. Methods: Ten commercial PDO feta cheeses from two geographic regions of Greece, Epirus and Thessaly, were analyzed by 16S metagenomic analysis. Results: The biodiversity of all the tested feta cheese samples consisted of five phyla, 17 families, 38 genera and 59 bacterial species. The dominant phylum identified was Firmicutes (49% of the species), followed by Proteobacteria (39% of the species), Bacteroidetes (7% of the species), Actinobacteria (4% of the species) and Tenericutes (1% of the species). Streptococcaceae and Lactobacillaceae were the most abundant families, in which starter cultures of lactic acid bacteria (LAB) belonged, but also 21 nonstarter lactic acid bacteria (NSLAB) were identified. Both geographical areas showed a distinctive microbiota fingerprint, which was ultimately overlapped by the application of starter cultures. In the rare biosphere of the feta cheese, Zobellella taiwanensis and Vibrio diazotrophicus, two Gram-negative bacteria which were not previously reported in dairy samples, were identified. Conclusions: The application of high-throughput DNA sequencing may provide a detailed microbial profile of commercial feta cheese produced with pasteurized milk.

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Section: Bacterial Diversity Of Feta Cheesesupporting

confidence: 91%

Characterization of Bacterial Microbiota of P.D.O. Feta Cheese by 16S Metagenomic Analysis

et al. 2021

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“…In certain instances, the abundance of genera was below 1%, mostly in Homemade samples 3 and 4, which presented the lowest species richness among all samples ( Figure 3 C and Figure 4 A). The presence of Debaryomyces , Kluyveromyces , Pichia and Candida genera in Feta has been reported in a number of studies as mentioned earlier [ 4 , 12 , 13 , 15 , 32 ].…”

Section: Resultsmentioning

confidence: 80%

“…In addition, it has been previously suggested that ripening conditions could lead to the selection of lactococcal populations [ 9 ]. Nevertheless, high abundances of lactococci in industrial Feta cheese samples has also been reported in three recent 16S rDNA metagenomics studies [ 32 , 33 , 34 ]. The higher richness in identified genera of the homemade samples may indicate lower hygienic conditions prevailing during cheese production when compared to the industrial ones ( Table 1 and Figure 2 A).…”

Section: Resultsmentioning

confidence: 81%

“…Briefly, 0.5 g of Feta cheese were washed with sterile distilled water, and fat was removed after centrifugation. Of note, similar amounts of Feta cheese samples have also been used for DNA extraction by others [ 32 , 33 ]. The pellets were resuspended in phosphate buffered saline (PBS) pH 7.4 and incubated at 65 °C for 10 min to inactivate DNAses that can degrade the extracted DNA.…”

Section: Methodsmentioning

confidence: 99%

“…Shotgun metagenomics may provide evidence about which microorganisms are present in the niche at a lower taxonomic level (i.e., at the species or subspecies level), but can also reveal their potential functional properties. Amplicon sequencing has been applied in Feta cheese samples before [ 32 , 33 , 34 ]. However, these studies along with all other studies focusing on the microbiology of Feta cheese relied on commercial, artisanal, or experimental Feta cheese samples produced on an industrial scale or in small-scale cheese making facilities.…”

Section: Introductionmentioning

confidence: 99%

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Comparison of the Microbiome of Artisanal Homemade and Industrial Feta Cheese through Amplicon Sequencing and Shotgun Metagenomics

et al. 2022

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Feta is the most renowned protected designation of origin (PDO) white brined cheese produced in Greece. The fine organoleptic characteristics and the quality of Feta rely on, among other factors, its overall microbial ecosystem. In this study, we employed 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing, as well as shotgun metagenomics, to investigate the microbiome of artisanal homemade and industrial Feta cheese samples from different regions of Greece, which has very rarely been investigated. 16S rDNA data suggested the prevalence of the Lactococcus genus in the homemade samples, while Streptococcus and Lactobacillus genera prevailed in the industrial control samples. Species identification deriving from shotgun metagenomics corroborated these findings, as Lactococcus lactis dominated two homemade samples while Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus were found to be dominating one industrial sample. ITS data revealed a complex diversity of the yeast population among the samples analyzed. Debaryomyces, Kluyveromyces, Cutaneotrichosporon, Pichia, Candida, and Rhodotorula were the major genera identified, which were distributed in a rather arbitrary manner among the different samples. Furthermore, a number of potential metagenome-assembled genomes (MAGs) could be detected among assembled shotgun bins. The overall analysis of the shotgun metagenomics supported the presence of different foodborne pathogens in homemade samples (e.g., Staphylococcus aureus, Listeria monocytogenes, Enterobacter cloacae, and Streptococcus suis), but with low to very low abundances. Concluding, the combination of both amplicon sequencing and shotgun metagenomics allowed us to obtain an in-depth profile of the artisanal homemade Feta cheese microbiome.

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