Development and application of a real-time PCR-based assay to enumerate total yeasts and Pichia anomala, Pichia guillermondii and Pichia kluyveri in fermented table olives

Rapid detection of Saccharomyces cerevisiae with boronic acid-decorated multivariate metal-organic frameworks and aptamers

Liquor brewing is a classic solid-substrate fermentation process with a unique brewing microbiome. As one of the most common fungi, Saccharomyces cerevisiae ferments saccharides and has been extensively applied in brewing production. Here, we present the facile fabrication of a selective, sensitive, and integrated fluorescent biosensor for S. cerevisiae detection. The proposed biosensor used aptamer-modified magnetic beads to specifically capture S. cerevisiae, and the enriched fungi were recognized and detected with boronic acid-decorated multivariate metal-organic frameworks. The biosensor allows rapid quantification of S. cerevisiae in the range of 10-106 CFU mL-1, showing excellent specificity and repeatability, and maintaining stable biosensing performance in long-term storage. The analytical ability of the proposed biosensor was successfully verified in distilled yeast and fermented grain samples spiked with S. cerevisiae.

Rapid Detection of Brettanomyces bruxellensis in Wine by Polychromatic Flow Cytometry

Brettanomyces bruxellensis is found in several fermented matrices and produces relevant alterations to the wine quality. The methods usually used to identify B. bruxellensis contamination are based on conventional microbiological techniques that require long procedures (15 days), causing the yeast to spread in the meantime. Recently, a flow cytometry kit for the rapid detection (1-2 h) of B. bruxellensis in wine has been developed. The feasibility of the method was assessed in a synthetic medium as well as in wine samples by detecting B. bruxellensis in the presence of other yeast species (Saccharomyces cerevisiae and Pichia spp.) and at the concentrations that produce natural contaminations (up to 10⁵ cells/mL), as well as at lower concentrations (10³-10² cells/mL). Wine samples naturally contaminated by B. bruxellensis or inoculated with four different strains of B. bruxellensis species together with Saccharomyces cerevisiae and Pichia spp., were analyzed by flow cytometry. Plate counts were carried out in parallel to flow cytometry. We provide evidence that flow cytometry allows the rapid detection of B. bruxellensis in simple and complex mixtures. Therefore, this technique has great potential for the detection of B. bruxellensis and could allow preventive actions to reduce wine spoilage.

Development of quantitative real-time PCR and digital droplet-PCR assays for rapid and early detection of the spoilage yeasts Saccharomycopsis fibuligera and Wickerhamomyces anomalus in bread

In the present study, for the first time, high sensitive quantitative polymerase chain reaction (qPCR) and digital droplet polymerase chain reaction (ddPCR) assays were developed to detect and quantify total eumycetes with potential application in several food matrices and to specifically determine the level of contamination by Saccharomycopsis fibuligera and Wickerhamomyces anomalus cells directly in bread. Among the candidate target genes used to develop the assays, car1 gene was chosen to detect the two spoilage yeasts S. fibuligera and W. anomalus. The specificity of the PCR assays was tested using purified genomic DNA from 36 bacterial and fungal strains. The sensitivity of the assays was defined by using tenfold serial dilutions of genomic DNA starting from 10⁶ cfu/mL to 1 cfu/mL of S. fibuligera and W. anomalus. Validation of the assays was achieved by enumeration of S. fibuligera and W. anomalus DNA copies from samples of artificially contaminated bread homogenates detecting up to 10 cfu/mL (0.06 ± 0.01 copies/μL) of W. anomalus by using ddPCR. In conclusion, the developed qPCR and ddPCR assays demonstrate strong performance in the early detection of S. fibuligera and W. anomalus in bread, representing promising tools for applying high-throughput approaches to regularly monitor bread quality.

The utility of iPBS retrotransposons markers to analyze genetic variation in yeast

Yeasts are one of the main organisms in the food industry and effective components of many ecosystems. The method for identifying and detecting certain yeast species or strains is a crucial step for the food industry and should be simple, reliable, fast, and inexpensive. In our study, inter-priming binding sites (iPBS) retrotransposon marker system was employed to elucidate the genetic variability at intraspecies and interspecies levels among 112 yeast strains belonging to eight species previously obtained from fermented foods. The molecular identification of yeast strains was firstly confirmed by sequencing the D1/D2 domain of the 26S rRNA. The eight selected retrotransposon-based primers produced 278 bands, all of which were polymorphic with an average of 34.75 polymorphic fragments per primer. The averages of polymorphism information contents and the resolving power values for the iPBS marker system were 0.23 and 10.11, respectively. The genetic parameters within each yeast species obtained from iPBS markers were observed as; the percentage of polymorphic loci for each species ranging from 19.23% to 71.21%, Nei's gene diversity from 0.085 to 0.228, while Shannon's information index values ranging from 0.125 to 0.349. The value of gene flow (0.09) and genetic variation among the populations (0.85) showed higher genetic variation among the species. UPGMA analyses demonstrated considerable genetic variability in the yeast strains, clustered them according to their species, and revealed the intraspecific variation. Each of the selected iPBS primer provided enough species-discrimination. Present evaluations suggest the utility of iPBS marker system to estimate the genetic variation of yeast strains. This study is a preliminary point for further studies on the identification methodology, and population genetics of yeast species having importance in the food industry with iPBS markers.

Detection of yeast Saccharomyces cerevisiae with ionic liquid mediated carbon dots

Hydrophobic nitrogen-doped carbon dots are prepared with energetic ionic liquid (1,3-dibutylimidazolium dicyandiamide, BbimDCN) as carbon source. A yield of as high as 58% is obtained for the carbon dots, shortly termed as BbimDCN-OCDs, due to the presence of thermal-instable N(CN)₂^- moiety. BbimDCN-OCDs exhibit favorable biocompability and excellent imaging capacity for fluorescence labelling of yeast cell Saccharomyces cerevisiae. In addition, chitosan-modified Dy³⁺-doped magnetic nanoparticles (shortly as Chitosan@Fe_2.75Dy_0.25O₄) with superparamagnetism are prepared. The electrostatic attraction between positively charged magnetic nanoparticles and negatively charged yeast cells facilitates exclusive recognition/isolation of S. cerevisiae. In practice, S. cerevisiae is labelled by BbimDCN-OCDs and adhered onto the Chitosan@Fe_2.75Dy_0.25O₄. The yeast/ BbimDCN-OCDs/Chitosan@Fe_2.75Dy_0.25O₄ composite is then isolated with an external magnet and the fluorescence from BbimDCN-OCDs incorporated in S. cerevisiae is monitored. The fluorescence intensity is linearly correlated with the content of yeast cell, showing a calibration graph of F = 3.01log[C]+11.7, offering a detection limit of 5×10² CFU/mL. S. cerevisiae content in various real sample matrixes are quantified by using this protocol.

Effect of the mechanical harvest of drupes on the quality characteristics of green fermented table olives

BACKGROUND

Because of damage caused by mechanical harvesting, the drupes for table olive production are traditionally hand harvested. Until now, no data have been available on the microbiological and chemical features of mechanically harvested drupes during fermentation.

RESULTS

Drupes mechanically harvested and inoculated with Lactobacillus pentosus OM13 were characterized by the lowest concentrations of potential spoilage microorganisms. On the other hand, drupes mechanically harvested and subjected to spontaneous fermentation showed the highest concentration of Enterobacteriaceae and pseudomonads during transformation. The lowest decrease of pH (4.20) was registered for the trials inoculated with the starter culture. Differences in terms of volatile organic compounds were estimated among trials. Multivariate analysis showed that the olives processed from the drupes mechanically harvested and inoculated with starter were closely related to control production (drupes manually harvested) in terms of microbiological and pH values. Sensory analysis evidenced negative evaluations only for the uninoculated trials.

CONCLUSION

Drupes mechanically harvested and subjected to a driven fermentation with Lactobacillus pentosus OM13 determined the production of table olives with appreciable organoleptic features. Thus mechanical harvesting performed using a trunk shaker equipped with an inverse umbrella and the addition of starter lactic acid bacteria represents a valuable alternative to manual harvesting for table olive production at the industrial level.

Selection of yeasts with multifunctional features for application as starters in natural black table olive processing

Yeasts are unicellular eukaryotic microorganisms with a great importance in the elaboration on many foods and beverages. In the last years, researches have focused their attention to determine the favourable effects that these microorganisms could provide to table olive processing. In this context, the present study assesses, at laboratory scale, the potential technological (resistance to salt, lipase, esterase and β-glucosidase activities) and probiotic (phytase activity, survival to gastric and pancreatic digestions) features of 12 yeast strains originally isolated from Greek natural black table olive fermentations. The multivariate classification analysis carried out with all information obtained (a total of 336 quantitative input data), revealed that the most promising strains (clearly discriminated from the rest of isolates) were Pichia guilliermondii Y16 (which showed overall the highest resistance to salt and simulated digestions) and Wickerhamomyces anomalus Y18 (with the overall highest technological enzymatic activities), while the rest of strains were grouped together in two clearly differentiated clusters. Thus, this work opens the possibility for the evaluation of these two selected yeasts as multifunctional starters, alone or in combination with lactic acid bacteria, in real table olive fermentations.

Yeasts in table olive processing: desirable or spoilage microorganisms?

Yeasts are unicellular eukaryotic microorganisms isolated from many foods, and are commonly found in table olive processing where they can play a double role. On one hand, these microorganisms can produce spoilage of fruits due to the production of bad odours and flavours, the accumulation of CO(2) leading to swollen containers, the clouding of brines, the softening of fruits and the degradation of lactic acid, which is especially harmful during table olive storage and packaging. But on the other hand, fortunately, yeasts also possess desirable biochemical activities (lipase, esterase, β-glucosidase, catalase, production of killer factors, etc.) with important technological applications in this fermented vegetable. Recently, the probiotic potential of olive yeasts has begun to be evaluated because many species are able to resist the passage through the gastrointestinal tract and show beneficial effects on the host. In this way, yeasts may improve consumers' health by decreasing cholesterol levels, inhibiting pathogens, degrading non assimilated compounds, producing antioxidants and vitamins, adhering to intestinal cells or by maintaining epithelial barrier integrity. Many yeast species, usually also found in table olive processing, such as Wicherhamomyces anomalus, Saccharomyces cerevisiae, Pichia membranifaciens and Kluyveromyces lactis, have been reported to exhibit some of these properties. Thus, the selection of the most appropriate strains to be used as starters, alone or in combination with lactic acid bacteria, is a promising research line to develop in a near future which might improve the added value of the commercialized product.

Microbiological and chemical profiles of naturally fermented table olives and brines from different Italian cultivars

Six naturally fermented (Greek-style) table olives of cultivars Itrana, Peranzana, Cellina di Nardò, Nocellara del Belice and Bella di Cerignola, as well as their corresponding brines, were studied by a combined strategy consisting of chemical, microbiological and molecular analyses. In particular, organic acids, sugars, polyphenols, fatty acids, biogenic amines and cultivable microbiota were detected by standard methods. Moreover, tyramine and histamine producing bacteria were evaluated by an original approach consisting of Reverse-Transcription (RT)-qPCR. At the end of the fermentation process, mesophilic lactobacilli and yeasts in brine represented the dominating biota, ranging from 6.25 to 7.84 log CFU/ml and from 6.5 to 7.56 log CFU/ml, respectively. Enterobacteriaceae and pathogens were undetectable in all the samples. In general, table olive preparations differed in chemical composition. In particular, C16:0 and C18:2c9,12 concentrations ranged from 9.9 to 18.8 % and from 5.4 to 15.4 % of total fatty acids, respectively. The main fatty acid detected was C18:1c9 while CLAc9, t11 was present only in traces. Polyphenol concentrations greatly differentiated the final product, depending on the cultivar. A low quantity of biogenic amines was found in some samples and biogenic amines producing bacteria were rapidly detectable by RT-qPCR.