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Wine reflects the specificity of a terroir, including the native microbiota. In contrast to the use of Saccharomyces cerevisiae commercial starters, a way to maintain wines’ microbial terroir identities, guaranteeing at the same time the predictability and reproducibility of the wines, is the selection of autochthonous Saccharomyces and non-Saccharomyces strains towards optimal enological characteristics for the chosen area of isolation. This field has been explored but there is a lack of a compendium covering the main methods to use. Autochthonous wine yeasts from different areas of Slovakia were identified and tested, in the form of colonies grown either on nutrient agar plates or in grape must micro-fermentations, for technological and qualitative enological characteristics. Based on the combined results, Saccharomyces cerevisiae PDA W 10, Lachancea thermotolerans 5-1-1 and Metschnikowia pulcherrima 125/14 were selected as potential wine starters. This paper, as a mixture of experimental and review contributions, provides a compendium of methods used to select autochthonous wine yeasts. Thanks to the presence of images, this compendium could guide other researchers in screening their own yeast strains for wine production.

Wine production is a complex procedure in which an important role is played by many microorganisms, particularly yeasts and bacteria. In modern wineries, alcoholic fermentation is usually carried out by adding microbial starter cultures of Saccharomyces cerevisiae strains for precisely controlled production. Nowadays, in the Slovak Republic, autochthonous vinification is getting more popular. The present article deals with the comparison of two vinification approaches, namely spontaneous fermentation and fermentation controlled by a standard commercial S. cerevisiae starter, from the point of view of microbiota dynamics and the chemical characteristics of the wines produced. The dynamics of microbial populations were determined during the fermentation process by a 16S and 28S rRNA next-generation sequencing approach. A profile of the volatile compounds during these fermentation processes was identified by solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS). In summary, the microbial diversity in the m1 phase (initial must) was higher, despite the presence of the starter culture. In the m3 phase (young wine), the microbiome profiles of both batches were very similar. It seems that the crucial phase in order to study the relationship of the microbiome and the resulting product should be based on the m2 phase (fermented must), where the differences between the autochthonous and inoculated batches were more evident.

A culture-independent method was developed for quantification of pathogenic bacteria in spices and herbs. The method is based on DNA extraction using cetyltrimethylammonium bromide (CTAB) and on real-time polymerase chain reaction (PCR). When evaluated with spices (black pepper, paprika) and herbs (oregano, parsley) artificially contaminated with Staphylococcus aureus, Salmonella enterica or Escherichia coli, the method demonstrated quantitative response with linear calibration lines and quantification limits of 102–104 CFU/g. The developed method is suitable for rapid microbiological analysis of spices and herbs, taking 8–9 h.

Various variants of ISO 6888-1:1999 and ISO 6888-3:2003 methods for the detection of Staphylococcus aureus were evaluated and improved for their application to conduct analysis in spices and herbs. Improvement substantiated in washing of the sample to remove compounds interfering with the analysis and in the use of PCR for final detection, instead of plating on Baird-Parker agar, to improve sensitivity at high backgrounds and to save time. The evaluation of the method variants was based on determination of the detection limit (LOD) using series of artificially contaminated spices (allspice, black pepper, cinnamon, nutmeg, paprika, vanilla) and herbs (basil, oregano, parsley, thyme). The method without enrichment, ISO 6888-1:1999, produced LODs of 103–105 CFU/g with no positive effect of washing the sample or use of PCR for final detection. The method with enrichment, ISO 6888-3:2003, had LOD of 100 CFU/g for basil, black pepper, paprika and parsley. If the washing step was added and PCR was used for final detection, LOD of 100 CFU/g was determined also for cinnamon, nutmeg and vanilla, and LOD of 101 CFU/g was determined for allspice. For oregano and thyme, which strongly inhibit the growth of S. aureus, an alternative enrichment-independent method based on direct DNA extraction coupled to real-time PCR may be advantageous.