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Volume 13
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10.3390/foods13071023
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Article

Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics

by
Natalia Tsouggou
1,
Aleksandra Slavko
1,
Olympia Tsipidou
2,
Anastasios Georgoulis
3,
Svetoslav G. Dimov
4,
Jia Yin
5,6,
Constantinos E. Vorgias
3,
John Kapolos
1,
Marina Papadelli
1 and
Konstantinos Papadimitriou
2,*
1
Department of Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece
2
Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, 18855 Athens, Greece
3
Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimioupolis-Zographou, 15784 Athens, Greece
4
Faculty of Biology, Sofia University “St. Kliment Ohridski”, 8, Dragan Tzankov Blvd., 1164 Sofia, Bulgaria
5
Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, College of Life Sciences, Hunan Normal University, Changsha 410081, China
6
Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, Changsha 410081, China
*
Author to whom correspondence should be addressed.
Foods 2024, 13(7), 1023; https://doi.org/10.3390/foods13071023
Submission received: 18 February 2024 / Revised: 17 March 2024 / Accepted: 21 March 2024 / Published: 27 March 2024
(This article belongs to the Special Issue New Insights into Milk and Dairy Products: Quality and Sustainability)
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Abstract

Sfela is a white brined Greek cheese of protected designation of origin (PDO) produced in the Peloponnese region from ovine, caprine milk, or a mixture of the two. Despite the PDO status of Sfela, very few studies have addressed its properties, including its microbiology. For this reason, we decided to investigate the microbiome of two PDO industrial Sfela cheese samples along with two non-PDO variants, namely Sfela touloumotiri and Xerosfeli. Matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI-TOF MS), 16S rDNA amplicon sequencing and shotgun metagenomics analysis were used to identify the microbiome of these traditional cheeses. Cultured-based analysis showed that the most frequent species that could be isolated from Sfela cheese were Enterococcus faecium, Lactiplantibacillus plantarum, Levilactobacillus brevis, Pediococcus pentosaceus and Streptococcus thermophilus. Shotgun analysis suggested that in industrial Sfela 1, Str. thermophilus dominated, while industrial Sfela 2 contained high levels of Lactococcus lactis. The two artisanal samples, Sfela touloumotiri and Xerosfeli, were dominated by Tetragenococcus halophilus and Str. thermophilus, respectively. Debaryomyces hansenii was the only yeast species with abundance > 1% present exclusively in the Sfela touloumotiri sample. Identifying additional yeast species in the shotgun data was challenging, possibly due to their low abundance. Sfela cheese appears to contain a rather complex microbial ecosystem and thus needs to be further studied and understood. This might be crucial for improving and standardizing both its production and safety measures.
Keywords: Sfela cheese; 16S rDNA; shotgun metagenomics; binning; lactic acid bacteria; microbiota Sfela cheese; 16S rDNA; shotgun metagenomics; binning; lactic acid bacteria; microbiota

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MDPI and ACS Style

Tsouggou, N.; Slavko, A.; Tsipidou, O.; Georgoulis, A.; Dimov, S.G.; Yin, J.; Vorgias, C.E.; Kapolos, J.; Papadelli, M.; Papadimitriou, K. Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics. Foods 2024, 13, 1023. https://doi.org/10.3390/foods13071023

AMA Style

Tsouggou N, Slavko A, Tsipidou O, Georgoulis A, Dimov SG, Yin J, Vorgias CE, Kapolos J, Papadelli M, Papadimitriou K. Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics. Foods. 2024; 13(7):1023. https://doi.org/10.3390/foods13071023

Chicago/Turabian Style

Tsouggou, Natalia, Aleksandra Slavko, Olympia Tsipidou, Anastasios Georgoulis, Svetoslav G. Dimov, Jia Yin, Constantinos E. Vorgias, John Kapolos, Marina Papadelli, and Konstantinos Papadimitriou. 2024. "Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics" Foods 13, no. 7: 1023. https://doi.org/10.3390/foods13071023

APA Style

Tsouggou, N., Slavko, A., Tsipidou, O., Georgoulis, A., Dimov, S. G., Yin, J., Vorgias, C. E., Kapolos, J., Papadelli, M., & Papadimitriou, K. (2024). Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics. Foods, 13(7), 1023. https://doi.org/10.3390/foods13071023

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