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Nova Biotechnologica et Chimica

The Journal of University of SS. Cyril and Methodius

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CiteScore 2016: 0.42

SCImago Journal Rank (SJR) 2015: 0.129
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1338-6905
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Metagenomic Analysis of Slovak Bryndza Cheese Using Next-Generation 16S rDNA Amplicon Sequencing

Matej Planý
  • Corresponding author
  • Department of Biology, University of SS. Cyril and Methodius, J. Herdu 2, Trnava, SK-917 01, Slovak Republic
  • Department of Microbiology and Molecular Biology, Food Research Institute NAFC, Priemyselná 4, 824 75 Bratislava 26, Slovak Republic
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Tomáš Kuchta
  • Department of Microbiology and Molecular Biology, Food Research Institute NAFC, Priemyselná 4, 824 75 Bratislava 26, Slovak Republic
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Katarína Šoltýs / Tomáš Szemes / Domenico Pangallo
  • Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovak Republic
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Peter Siekel
  • Department of Biology, University of SS. Cyril and Methodius, J. Herdu 2, Trnava, SK-917 01, Slovak Republic
  • Department of Microbiology and Molecular Biology, Food Research Institute NAFC, Priemyselná 4, 824 75 Bratislava 26, Slovak Republic
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2016-08-04 | DOI: https://doi.org/10.1515/nbec-2016-0003

Abstract

Knowledge about diversity and taxonomic structure of the microbial population present in traditional fermented foods plays a key role in starter culture selection, safety improvement and quality enhancement of the end product. Aim of this study was to investigate microbial consortia composition in Slovak bryndza cheese. For this purpose, we used culture-independent approach based on 16S rDNA amplicon sequencing using next generation sequencing platform. Results obtained by the analysis of three commercial (produced on industrial scale in winter season) and one traditional (artisanal, most valued, produced in May) Slovak bryndza cheese sample were compared. A diverse prokaryotic microflora composed mostly of the genera Lactococcus, Streptococcus, Lactobacillus, and Enterococcus was identified. Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris were the dominant taxons in all tested samples. Second most abundant species, detected in all bryndza cheeses, were Lactococcus fujiensis and Lactococcus taiwanensis, independently by two different approaches, using different reference 16S rRNA genes databases (Greengenes and NCBI respectively). They have been detected in bryndza cheese samples in substantial amount for the first time. The narrowest microbial diversity was observed in a sample made with a starter culture from pasteurised milk. Metagenomic analysis by high-throughput sequencing using 16S rRNA genes seems to be a powerful tool for studying the structure of the microbial population in cheeses.

Keywords: Lactic acid bacteria; Bryndza cheese; Next-generation sequencing; metagenomics; 16S rRNA genes

References

  • ALEGRIA, A., SZCZESNY, P., MAYO, B., BARDOWSKI, J., KOWALCZYK, M.: Biodiversity in Oscypek, a traditional Polish cheese, determined by culturedependent and -independent approaches. Appl. Environ. Microbiol., 78, 2012, 1890-1898.Web of ScienceCrossrefGoogle Scholar

  • ALTSCHUL, S. F., GISH, W., MILLER, W., MYERS, E. W., AND LIPMAN, D. J.: basic local alignment search tool. J. Mol. Biol., 215, 1990, 403-410.Google Scholar

  • BERTA, G., CHEBEŇOVÁ, V., BREŽNÁ, B., PANGALLO, D., VALÍK, Ľ., KUCHTA, T.: Identification of lactic acid bacteria in Slovakian bryndza cheese. J. Food Nutr. Res., 48, 2009, 65-71.Google Scholar

  • BURDOVÁ, O.: Legislative framework of sheep milk -the support of health risk decreasing. Slovak Vet. J. 22, 1997, 202-204.Google Scholar

  • CAPLICE, E., FITZGERALD, G. F.: Food fermentations: role of microorganisms in food production and preservation. Int. J. Food Microbiol., 50, 1999, 131-149.Google Scholar

  • COPPOLA, S., BLAIOTTA, G., ERCOLINI, D., AND MOSCHETTI, G.: Molecular evaluation of microbial diversity occuring in different types of Mozzarella cheese. J. Appl. Microbiol., 90, 2001, 414- 420.CrossrefGoogle Scholar

  • DeSANTIS, T. Z., HUGENHOLTZ, P., LARSEN, N., ROJAS, M., BRODIE, E. L., KELLER, K., HUBER, T., DALEVI, D., HU, P., ANDERSEN,G. L.: Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol., 27, 2006, 5069-72.Google Scholar

  • HOLKO, I., BISOVA, T., HOLKOVA, Z., KMET, V.: Virulence markers of Escherichia coli strains isolated from traditional cheeses made from unpasteurised sheep milk in Slovakia. Food Control, 17, 2006, 393- 396.CrossrefGoogle Scholar

  • HUSON, D. H, MITRA, S., RUSCHEWEYH, H-J., WEBER, N., SCHUSTER, S. C..: Integrative analysis of environmental sequences using MEGAN 4, Genome Res., 21, 2011, 1552-1560.Web of ScienceGoogle Scholar

  • CHEBEŇOVÁ-TURCOVSKÁ, V., ŽENIŠOVÁ, K., KUCHTA, T., PANGALLO, D., BREŽNÁ, B.: Culture-independent detection of microorganisms in traditional Slovakian bryndza cheese. Int. J. Food Microbiol., 150, 2011, 73-78.Web of ScienceGoogle Scholar

  • CHEN, C., KHALEEL, SS., HUANG, H., WU, CH.: Software for pre-processing Illumina next-generation sequencing short read sequences. Source Code Biol. Med., 9, 2014, 1-11.Google Scholar

  • ERCOLINI, D. : High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology. Appl. Environ. Microbiol., 79, 2013, 3148- 3155CrossrefGoogle Scholar

  • ERCOLINI, D., DE FILIPPIS, F., LA STORIA, A., IACONO, M.: “Remake” by High-Throughput Sequencing of the Microbiota Involved in the Production of Water Buffalo Mozzarella Cheese. Appl. Environ. Microbiol., 78, 2012, 8142-8145.Google Scholar

  • EWING, B. GREEN, P.: Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities. Genome Res., 8, 1998, 186-194.CrossrefGoogle Scholar

  • GHYSELINCK, J., PFEIFFER, S., HEYLEN, K., SESSITSCH, A., DE VOS, P.: The Effect of Primer Choice and Short Read Sequences on the Outcome of 16S rRNA Gene Based Diversity Studies. PLoS ONE, 8, 2013, e 71360.Google Scholar

  • JURKOVIČ, D., KRIZKOVÁ, L., DUSINSKÝ, R., BELICOVÁ, A., SOJKA, M., KRAJČOVIČ, J., EBRINGER, L.: Identification and characterization of enterococci from bryndza cheese. Lett. Appl. Microbiol., 42, 2006, 553-559.Google Scholar

  • LAURENČÍK, M., SULO, P., SLÁVIKOVÁ, E., PIECKOVÁ, E., SEMAN, M., EBRINGER, L.: The diversity of eukaryotic microbiota in the traditional Slovak sheep cheese - Bryndza. Int. J. Food Microbiol., 127, 2008, 176-179.Google Scholar

  • LEROY, F., De VUYST, L.: Lactic acid bacteria as functional starter cultures for the food fermentation industry. Trends Food Sci. Tech., 15, 2004, 67-78.Google Scholar

  • LUSK, T. S., OTTESEN, A. R., WHITE, J. R., ALLARD, M. W., BROWN, E. W., KASE, J. A.: Characterization of microflora in Latin-style cheeses by nextgeneration sequencing technology. BMC Microbiol., 12, 2012, 254.Web of ScienceCrossrefGoogle Scholar

  • MASOUD, W., VOGENSEN, F. K., LILLEVANG, S., ABU AL-SOUD, W., SORENSEN, S. J., JAKOBSEN, M.: The fate of indigenous microbiota, starter cultures, Escherichia coli, Listeria innocua and Staphylococcus aureus in Danish raw milk and cheeses determined by pyrosequencing and quantitative real time (qRT)-PCR. J. Food Microbiol., 153, 2012, 192-202.Google Scholar

  • MAŠLANKOVÁ, J., PILIPČINCOVÁ, I., TKÁČIKOVÁ, L.: Pheno- and genotyping of Staphylococcus aureus isolates of sheep origin. Acta Vet. Brno, 78, 2009, 345-352.CrossrefWeb of ScienceGoogle Scholar

  • PANGALLO, D., ŠAKOVÁ, N., KOREŇOVÁ, J., PUŠKÁROVÁ, A., KRAKOVÁ, L., VALÍK, L., KUCHTA, T.: Microbial diversity and dynamics during the production of May bryndza cheese. Int. J. Food Microbiol., 170, 2014, 38-43.Google Scholar

  • SÁDECKÁ, J., KOLEK, E., PANGALLO, D., VALÍK, L., KUCHTA, T.: Principal volatile odorants and dynamics of their formation during the production of May bryndza cheese. Food Chem., 150, 2014, 301-306.Web of ScienceGoogle Scholar

  • SULO, P., LAURENČÍK, M., POLÁKOVÁ, S., MINÁRIK, G., SLÁVIKOVÁ, E.: Geotrichum bryndzae sp. nov., a novel asexual arthroconidial yeast species related to the genus Galactomyces. Int. J. Syst. Evol. Microbiol., 59, 2009, 2370-2374.Web of ScienceGoogle Scholar

  • QUIGLEY, L., O’SULLIVAN, O., BERESFORD, T. P., ROSS, R. P., FITZGERALD, G. F., COTTER, P. D.: High-throughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses. Appl. Environ. Microbiol., 78, 2012, 5717-5723.Google Scholar

About the article

Received: 2015-11-27

Accepted: 2016-05-05

Published Online: 2016-08-04

Published in Print: 2016-06-01


Citation Information: Nova Biotechnologica et Chimica, Volume 15, Issue 1, Pages 23–34, ISSN (Online) 1338-6905, DOI: https://doi.org/10.1515/nbec-2016-0003.

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© by Matej Planý. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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