Rapid identification and enumeration of Saccharomyces cerevisiae cells in wine by real-time PCR

Potential applications of pulsed electric field in the fermented wine industry

Fermented wine refers to alcoholic beverages with complex flavor substances directly produced by raw materials (fruit or rice) through microbial fermentation (yeast and bacteria). Its production steps usually include saccharification, fermentation, filtration, sterilization, aging, etc., which is a complicated and time-consuming process. Pulsed electric field (PEF) is a promising non-thermal food processing technology. Researchers have made tremendous progress in the potential application of PEF in the fermented wine industry over the past few years. The objective of this paper is to systematically review the achievements of PEF technology applied to the winemaking and aging process of fermented wine. Research on the application of PEF in fermented wine suggests that PEF treatment has the following advantages: (1) shortening the maceration time of brewing materials; (2) promoting the extraction of main functional components; (3) enhancing the color of fermented wine; (4) inactivating spoilage microorganisms; and (5) accelerating the formation of aroma substances. These are mainly related to PEF-induced electroporation of biomembranes, changes in molecular structure and the occurrence of chemical reactions. In addition, the key points of PEF treatments for fermented wine are discussed and some negative impacts and research directions are proposed.

Saccharomyces cerevisiae Diversity in Arbutus unedo L. Fermentations in Association with the Volatile and Sensory Similarities of the Distillates

The fermentation of Arbutus unedo L. fruit is traditionally carried out in the production of spirits. The present study followed the spontaneous fermentation of A. unedo fruit harvested in October and December 2019 by two producers from the central region of Portugal. The microbiota was studied, and although a great diversity of indigenous yeasts was found, S. cerevisiae isolates could still be grouped into eight clusters, and a good separation between producers was achieved. Based on the results of a multivariate analysis of the physical-chemical and volatile composition of the distillates, a distinction between the distillates from the two producers was determined. Moreover, these findings are corroborated by the similarities in flavor that were found. Along with the variability found in the distillates, S. cerevisiae isolates could be clustered and associated with each producer. On the other hand, the differentiation of the harvesting period was not so clear. The characterization of the indigenous yeasts associated with the fermentation process of Arbutus unedo L. fruit can serve as an important contribution to the preservation of the specific characteristics of its distillates.

Yeast Biodiversity in Vineyard during Grape Ripening: Comparison between Culture Dependent and NGS Analysis

In this study, the evolution of the yeast microflora present on the berry surface, during the ripening of Barbera grapes, was monitored. Sampling was performed in three vineyards located in the “Nizza” Barbera d’Asti DOC zone and different methodologies have been employed. A culture-dependent method based on the identification of strains grown on solid media by ARDRA (Amplified Ribosomal DNA Restriction Analysis) and the D1-D2 domain of ribosomal 26S DNA capillary sequencing was coupled to NGS (Next Generation Sequencing) targeting ITS (Internal Transcribed Sequence) amplicons with the Illumina MiSeq platform. By using culture-dependent techniques, the most frequently detected species was the yeast-like fungus Aureobasidium pullulans, which was dominant in the culturable fraction. Among yeasts, the presence of oligotrophic basidiomycetes such as Cryptococcus spp., Rhodotorula graminis and Sporidiobolus pararoseus was observed at the beginning of ripening. Afterward, upon approaching the harvest, a succession of oxidative or weakly fermentative copiotrophic species occurs, such as Saturnispora diversa, Issatchenkia terricola, Hanseniaspora opuntiae, Starmerella bacillaris and Hanseniaspora uvarum. The massive sequencing revealed a larger number of species, respect to the culture-dependent data. Comparing the two different approaches used in this work, it is possible to highlight some similarities since Aureobasidium, Rhodotorula and Sporobolomyces were detected by both methods. On the contrary, genera Hanseniaspora, Issatchenkia and Saturnispora were revealed by culture-dependent methods, but not by NGS, while Saccharomyces spp. were identified, with low frequency, only by NGS. The integrated application of NGS sequencing and culture-dependent techniques provides a comprehensive view of mycodiversity in the wine-growing environment, especially for yeasts with low abundance.

Molecular tools for the analysis of the microbiota involved in malolactic fermentation: from microbial diversity to selection of lactic acid bacteria of enological interest

Winemaking is a complex process involving two successive fermentations: alcoholic fermentation, by yeasts, and malolactic fermentation (MLF), by lactic acid bacteria (LAB). During MLF, LAB can contribute positively to wine flavor through decarboxylation of malic acid with acidity reduction and other numerous enzymatic reactions. However, some microorganisms can have a negative impact on the quality of the wine through processes such as biogenic amine production. For these reasons, monitoring the bacterial community profiles during MLF can predict and control the quality of the final product. In addition, the selection of LAB from a wine-producing area is necessary for the formulation of native malolactic starter cultures well adapted to local winemaking practices and able to enhance the regional wine typicality. In this sense, molecular biology techniques are fundamental tools to decipher the native microbiome involved in MLF and to select bacterial strains with potential to function as starter cultures, given their enological and technological characteristics. In this context, this work reviews the different molecular tools (both culture-dependent and -independent) that can be applied to the study of MLF, either in bacterial isolates or in the microbial community of wine, and of its dynamics during the process.

Microbial Variability of Commercial Equine Probiotics

Probiotics are defined as live microorganisms that confer a health benefit to the host when administered in adequate amounts, therefore the presence of viable microorganisms is essential. Previous studies reported inconsistencies when comparing contents of probiotics marketed for use in animals with label claims. However, to the author's knowledge the variability of the same product between different lots has yet to be evaluated. The objective of this observational study was to evaluate the content and inter-lot variability of commercial equine probiotic products using culture dependent and independent techniques. Eleven probiotics marketed for use in horses were evaluated for microbial content using culture-dependent and independent techniques. The content was then compared to microorganisms listed and quantities on the label of the probiotic. Statistical analyses were performed using a Kruskal-Wallis test. None of the 11 probiotics met their label claim. Nine of the 11 did not have statistically significant inter-lot variability. Several products lacked microorganisms listed on the label based on both culture and polymerase chain reaction (PCR) analyses.

Emerging Non-Thermal Technologies as Alternative to SO2 for the Production of Wine

SO₂ is an antioxidant and selective antimicrobial additive, inhibiting the growth of molds in the must during the early stages of wine production, as well as undesirable bacteria and yeasts during fermentation, thus avoiding microbial spoilage during wine production and storage. The addition of SO₂ is regulated to a maximum of 150–350 ppm, as this chemical preservative can cause adverse effects in consumers such as allergic reactions. Therefore, the wine industry is interested in finding alternative strategies to reduce SO₂ levels, while maintaining wine quality. The use of non-thermal or cold pasteurization technologies for wine preservation was reviewed. The effect of pulsed electric fields (PEF), high pressure processing (HPP), power ultrasound (US), ultraviolet irradiation (UV), high pressure homogenization (HPH), filtration and low electric current (LEC) on wine quality and microbial inactivation was explored and the technologies were compared. PEF and HPP proved to be effective wine pasteurization technologies as they inactivate key wine spoilage yeasts, including Brettanomyces, and bacteria in short periods of time, while retaining the characteristic flavor and aroma of the wine produced. PEF is a promising technology for the beverage industry as it is a continuous process, requiring only microseconds of processing time for the inactivation of undesirable microbes in wines, with commercial scale, higher throughput production potential.

Analysis of methods for quantifying yeast cell concentration in complex lignocellulosic fermentation processes

Cell mass and viability are tightly linked to the productivity of fermentation processes. In 2^nd generation lignocellulose-based media quantitative measurement of cell concentration is challenging because of particles, auto-fluorescence, and intrinsic colour and turbidity of the media. We systematically evaluated several methods for quantifying total and viable yeast cell concentrations to validate their use in lignocellulosic media. Several automated cell counting systems and stain-based viability tests had very limited applicability in such samples. In contrast, manual cell enumeration in a hemocytometer, plating and enumeration of colony forming units, qPCR, and in situ dielectric spectroscopy were further investigated. Parameter optimization to measurements in synthetic lignocellulosic media, which mimicked typical lignocellulosic fermentation conditions, resulted in statistically significant calibration models with good predictive capacity for these four methods. Manual enumeration of cells in a hemocytometer and of CFU were further validated for quantitative assessment of cell numbers in simultaneous saccharification and fermentation experiments on steam-exploded wheat straw. Furthermore, quantitative correlations could be established between these variables and in situ permittivity. In contrast, qPCR quantification suffered from inconsistent DNA extraction from the lignocellulosic slurries. Development of reliable and validated cell quantification methods and understanding their strengths and limitations in lignocellulosic contexts, will enable further development, optimization, and control of lignocellulose-based fermentation processes.

On metal and 'spoiled' wine: analysing psimythion (synthetic cerussite) pellets (5th-3rd centuries BCE) and hypothesising gas-metal reactions over a fermenting liquid within a Greek pot

A Pb-based synthetic mineral referred to as psimythion (pl. psimythia) was manufactured in the Greek world at least since the 6th c BCE and routinely by the 4th c BCE. Theophrastus (On Stones, 56) describes its preparation from metallic Pb suspended over a fermenting liquid. Psimythion is considered the precursor of one of western art's most prominent white pigments, i.e. lead white (basic lead carbonate or synthetic hydrocerussite). However, so far, and for that early period, published analyses of psimythia suggest that they consisted primarily of synthetic cerussite. In this paper, we set out to investigate how it was possible to manufacture pure cerussite, to the near exclusion of other phases. We examined the chemical and mineralogical composition (pXRF/XRD) of a small number of psimythion pellets found within ceramic pots (pyxis) from Athens and Boeotia (5th-4th c BCE) in the collection of the National Archaeological Museum (NAM), Athens. Analyses showed that the NAM pellets consisted primarily of Pb/cerussite with small amounts of Ca (some samples) and a host of metallic trace elements. We highlight the reference in the Theophrastus text to 'spoiled wine' (oxos), rather than 'vinegar', as has been previously assumed, the former including a strong biotic component. We carried out DNA sequencing of the pellets in an attempt to establish presence of microorganisms (Acetic Acid Bacteria). None was found. Subsequently, and as a working hypothesis, we propose a series of (biotic/abiotic) reactions which were likely to have taken place in the liquid and vapour phases and on the metal surface. The hypothesis aims to demonstrate that CO₂ would be microbially induced and would increase, as a function of time, resulting in cerussite forming over and above hydrocerussite/other Pb-rich phases. Psimythion has for long been valued as a white pigment. What has perhaps been not adequately appreciated is the depth of empirical understanding from the part of psimythion manufacturers of the reactions between abiotic and biotic components within 'oxos'/pot, as key drivers of minerals synthesis. Ultimately, psimythion manufacture may rest in understanding the nature of 'oxos', antiquity's relatively little researched strongest acid.

Non-sterile fermentation of food waste with indigenous consortium and yeast - Effects on microbial community and product spectrum

This work presents examples of non-sterile mixed culture fermentation of food waste with a cultivated indigenous consortium (IC) gained from food waste, which produces lactic and acetic acids, combined with Saccharomyces cerevisiae, which produces ethanol. All results are flanked by microbial analysis to monitor changes in microbial community. At pH 6 and inoculated with yeast or IC, or both mixed sugars conversion was equal to 71%, 51%, or 67%, respectively. Under pH unregulated conditions metabolic yields were 71%, 67%, or up to 81%. While final titer of acetic acid was not affected by pH (100-200 mM), ethanol and lactic acid titers were. Using mixed culture and pH 6, sugars were almost equally used for formation of ethanol and lactic acid (400-500 mM). However, under pH unregulated conditions 80% of the substrate was converted into ethanol (900-1000 mM).

Real-time PCR assays for the quantification of native yeast DNA in grape berry and fermentation extracts

Native yeasts comprise part of the microbial community in grape vineyards and play roles in alcoholic fermentation and wine quality. Monitoring populations of native yeast in vineyards, during fermentation and after bottling will provide viticulturalists and oenologists with information needed to help control spoilage and to enhance desirable wine properties. This is especially crucial for low-intervention winemaking, in which fermentation is driven by native rather than starter microbes. In this study, we report real-time polymerase chain reaction (qPCR) assays for rapid quantification of seven grape yeast species or species combinations that occur in vineyards of Washington State and throughout the world. The assays targeted Candida californica, Curvibasidium pallidicorallinum, Metschnikowia spp., Meyerozyma caribbica/Me. guilliermondii, and Saccharomyces cerevisiae/S. bayanus. We also developed assays for the spoilage yeast Brettanomyces bruxellensis, and the yeast-like fungus Aureobasidium pullulans. Primers were designed for sequences in the internal transcribed spacer (ITS) and large ribosome subunit (LSU) gene. Known populations of yeast cells, added to fermentation extract, were significantly correlated to amounts of purified DNA in picograms (pg) for most of the yeasts; exceptions were A. pullulans and Cu. pallidicorallinum. The utility of the Metschnikowia, Meyerozyma and Saccharomyces assays was further validated by good correlations (R² = 0.75-0.83) between the number of target sequences and pg of DNA from qPCR for selected vineyard and fermentation samples. Overall, the assays will aid in species identification and monitoring of specific yeasts from cultures, vineyards and fermentation samples. Topics: Food Microbiology, Microbiological Method.

Disposable amperometric immunosensor for Saccharomyces cerevisiae based on carboxylated graphene oxide-modified electrodes

A sensitive and disposable amperometric immunosensor for Saccharomyces cerevisiae was constructed by using carbon screen-printed electrodes modified with propionic acid-functionalized graphene oxide as transduction element. The affinity-based biosensing interface was assembled by covalent immobilization of a specific polyclonal antibody on the carboxylate-enriched electrode surface via a water-soluble carbodiimide/N-hydroxysuccinimide coupling approach. A concanavalin A-peroxidase conjugate was further used as signaling element. The immunosensor allowed the amperometric detection of the yeast in buffer solution and white wine samples in the range of 10-10⁷ CFU/mL. This electroanalytical device also exhibited low detection limit and high selectivity, reproducibility, and storage stability. The immunosensor was successfully validated in spiked white wine samples.

Yeast Monitoring of Wine Mixed or Sequential Fermentations Made by Native Strains from D.O. "Vinos de Madrid" Using Real-Time Quantitative PCR

There is an increasing trend toward understanding the impact of non-Saccharomyces yeasts on the winemaking process. Although Saccharomyces cerevisiae is the predominant species at the end of fermentation, it has been recognized that the presence of non-Saccharomyces species during alcoholic fermentation can produce an improvement in the quality and complexity of the final wines. A previous work was developed for selecting the best combinations between S. cerevisiae and five non-Saccharomyces (Torulaspora delbrueckii, Schizosaccharomyces pombe, Candida stellata, Metschnikowia pulcherrima, and Lachancea thermotolorans) native yeast strains from D.O. "Vinos de Madrid" at the laboratory scale. The best inoculation strategies between S. cerevisiae and non-Saccharomyces strains were chosen to analyze, by real-time quantitative PCR (qPCR) combined with the use of specific primers, the dynamics of inoculated populations throughout the fermentation process at the pilot scale using the Malvar white grape variety. The efficiency of the qPCR system was verified independently of the samples matrix, founding the inoculated yeast species throughout alcoholic fermentation. Finally, we can validate the positive effect of selected co-cultures in the Malvar wine quality, highlighting the sequential cultures of T. delbrueckii CLI 918/S. cerevisiae CLI 889 and C. stellata CLI 920/S. cerevisiae CLI 889 and, mixed and sequential cultures of L. thermotolerans 9-6C combined with S. cerevisiae CLI 889.

Cells-qPCR as a direct quantitative PCR method to avoid microbial DNA extractions in grape musts and wines

A novel quantitative PCR assay called Cells-qPCR has been developed for the rapid detection and quantification of yeasts, lactic acid bacteria (LAB) and acetic acid bacteria (AAB) directly from grape must and wine that does not require DNA extraction. The assay was tested on Brettanomyces bruxellensis, Saccharomyces cerevisiae, Lactobacillus plantarum, Oenococcus oeni, Acetobacter aceti and Gluconobacter oxydans in culture media, and in white and red grape musts and wines. Standard curves were constructed from DNA and cells for the six target species in all the matrices. Good efficiencies were obtained for both when comparing DNA and cells standard curves. No reaction inhibition was observed between matrices for each species. Cells quantification was linear over a range of cell concentrations (7, 5 or 4 orders of magnitude) and detected as few as one cell per reaction in all the matrices. The developed Cells-qPCR assay is a robust, reliable, fast and specific method to detect and quantify different yeasts, LAB and AAB species in grape must and wine that avoids DNA extraction and overcomes the presence of inhibitors like polyphenols and ethanol.

Gallbladder-derived surfactant protein D regulates gut commensal bacteria for maintaining intestinal homeostasis

The commensal microbiota within the gastrointestinal tract is essential in maintaining homeostasis. Indeed, dysregulation in the repertoire of microbiota can result in the development of intestinal immune-inflammatory diseases. Further, this immune regulation by gut microbiota is important systemically, impacting health and disease of organ systems beyond the local environment of the gut. What has not been explored is how distant organs might in turn shape the microbiota via microbe-targeted molecules. Here, we provide evidence that surfactant protein D (SP-D) synthesized in the gallbladder and delivered into intestinal lumen binds selectively to species of gut commensal bacteria. SP-D-deficient mice manifest intestinal dysbiosis and show a susceptibility to dextran sulfate sodium-induced colitis. Further, fecal transfer from SP-D-deficient mice to wild-type, germ-free mice conveyed colitis susceptibility. Interestingly, colitis caused a notable increase in Sftpd gene expression in the gallbladder, but not in the lung, via the activity of glucocorticoids produced in the liver. These findings describe a unique mechanism of interorgan regulation of intestinal immune homeostasis by SP-D with potential clinical implications such as cholecystectomy.

Genetic Polymorphism in Wine Yeasts: Mechanisms and Methods for Its Detection

The processes of yeast selection for using as wine fermentation starters have revealed a great phenotypic diversity both at interspecific and intraspecific level, which is explained by a corresponding genetic variation among different yeast isolates. Thus, the mechanisms involved in promoting these genetic changes are the main engine generating yeast biodiversity. Currently, an important task to understand biodiversity, population structure and evolutionary history of wine yeasts is the study of the molecular mechanisms involved in yeast adaptation to wine fermentation, and on remodeling the genomic features of wine yeast, unconsciously selected since the advent of winemaking. Moreover, the availability of rapid and simple molecular techniques that show genetic polymorphisms at species and strain levels have enabled the study of yeast diversity during wine fermentation. This review will summarize the mechanisms involved in generating genetic polymorphisms in yeasts, the molecular methods used to unveil genetic variation, and the utility of these polymorphisms to differentiate strains, populations, and species in order to infer the evolutionary history and the adaptive evolution of wine yeasts, and to identify their influence on their biotechnological and sensorial properties.

Hypocholesterolemic activity of indigenous probiotic isolate Saccharomyces cerevisiae ARDMC1 in a rat model

The aim of this study was to investigate probiotic attributes of Saccharomyces cerevisiae ARDMC1 isolated from traditional rice beer starter cake and its hypocholesterolemic effects on Wistar rats fed a high-cholesterol diet. The indigenous isolate ARDMC1 showed potential probiotic characteristics such as tolerance to simulated gastrointestinal stress conditions, autoaggregation properties, and adhesion to intestinal epithelium Caco-2 cell line. In addition, ARDMC1 isolate exhibited in vitro cholesterol assimilation properties in media supplemented with cholesterol. Furthermore, administration of probiotic isolate to rats fed a hypercholesterolemic diet resulted in significant reduction of serum total cholesterol, low-density lipoprotein cholesterol, and triglyceride at the end of 42 days. The present study envisages ARDMC1 as a promising starter culture for the preparation of functional foods with properties to combat cardiovascular diseases.

Rational and combinatorial approaches to engineering styrene production by Saccharomyces cerevisiae

BACKGROUND

Styrene is an important building-block petrochemical and monomer used to produce numerous plastics. Whereas styrene bioproduction by Escherichia coli was previously reported, the long-term potential of this approach will ultimately rely on the use of hosts with improved industrial phenotypes, such as the yeast Saccharomyces cerevisiae.

RESULTS

Classical metabolic evolution was first applied to isolate a mutant capable of phenylalanine over-production to 357 mg/L. Transcription analysis revealed up-regulation of several phenylalanine biosynthesis pathway genes including ARO3, encoding the bottleneck enzyme DAHP synthase. To catalyze the first pathway step, phenylalanine ammonia lyase encoded by PAL2 from A. thaliana was constitutively expressed from a high copy plasmid. The final pathway step, phenylacrylate decarboxylase, was catalyzed by the native FDC1. Expression of FDC1 was naturally induced by trans-cinnamate, the pathway intermediate and its substrate, at levels sufficient for ensuring flux through the pathway. Deletion of ARO10 to eliminate the competing Ehrlich pathway and expression of a feedback-resistant DAHP synthase encoded by ARO4K229L preserved and promoted the endogenous availability precursor phenylalanine, leading to improved pathway flux and styrene production. These systematic improvements allowed styrene titers to ultimately reach 29 mg/L at a glucose yield of 1.44 mg/g, a 60% improvement over the initial strain.

CONCLUSIONS

The potential of S. cerevisiae as a host for renewable styrene production has been demonstrated. Significant strain improvements, however, will ultimately be needed to achieve economical production levels.

Use of propidium monoazide for the enumeration of viable Brettanomyces bruxellensis in wine and beer by quantitative PCR

Brettanomyces bruxellensis is a current problem in winemaking all over the world, and the question if B. bruxellensis has a positive or negative impact on wine is one of the most controversial discussions in the world. The presence of live B. bruxellensis cells represents the risk of growth and an increase in cell numbers, which is related to the potential production of volatile phenols. In this work, the optimisation of a PMA-quantitative PCR (qPCR) method to enumerate only viable cells was carried out using the standard strain B. bruxellensis DSMZ 70726. The obtained detection limits were 0.83 log CFU/mL in red wine, 0.63 log CFU/mL in white wine and 0.23 log CFU/mL in beer. Moreover, the quantification was also performed by Reverse Transcription quantitative PCR (RT-qPCR), and the results showed a higher detection limit for all of the trials.

High content of biogenic amines in Pecorino cheeses

Pecorino refers to Italian cheeses made exclusively from raw or pasteurized ewes' milk, characterized by a high content of fat matter and it is mainly produced in the Middle and South of Italy by traditional procedures. The autochthonous microbiota plays an important role in the organoleptic traits of Pecorino cheese and it can influence biogenic amines (BA) content. The aim of this study was to characterize from microbiological and chemical point of view 12 randomly purchased commercial cheeses produced in Abruzzo region. Moreover, the BA content and the bacteria showing a decarboxylating activity were detected. For this purpose, a real-time quantitative PCR (qPCR) was applied to evaluate histamine and tyramine-producers. The samples were well differentiated for microbial groups composition, such as aerobic mesophilic bacteria, Enterobacteriaceae, coagulase-negative staphylococci, yeasts, enterococci, mesophilic and thermophilic lactobacilli. Pathogens such as Salmonella spp., Listeria monocytogenes and Escherichia coli O157:H7 were absent in all samples. In most samples the content of BA resulted to be high, with prevalence of histamine and tyramine. In particular, total BA content reached 5861 mg/kg in Pecorino di Fossa cheese. The qPCR method resulted to be very useful to understand the role of autochthonous Pecorino cheese microbiota on BA accumulation in many different products. In fact, since the ability of microorganisms to decarboxylate aminoacids is highly variable being in most cases strain-specific, the detection of bacteria possessing this activity is important to estimate the risk of BA cheese content.

Advances in the control of wine spoilage by Zygosaccharomyces and Dekkera/Brettanomyces

Understanding the characteristics of yeast spoilage, as well as the available control technologies, is vital to producing consistent, high-quality wine. Zygosaccharomyces bailii contamination may result in refermentation and CO2 production in sweet wines or grape juice concentrate, whereas Brettanomyces bruxellensis spoilage often contributes off-odors and flavors to red wines. Early detection of these yeasts by selective/differential media or genetic methods is important to minimize potential spoilage. More established methods of microbial control include sulfur dioxide, dimethyl dicarbonate, and filtration. Current research is focused on the use of chitosan, pulsed electric fields, low electric current, and ultrasonics as means to protect wine quality.

Quantitative PCR: an appropriate tool to detect viable but not culturable Brettanomyces bruxellensis in wine

Quantitative PCR as a tool has been used to detect Brettanomyces bruxellensis directly from wine samples. Accurate and timely detection of this yeast is important to prevent unwanted spoilage of wines and beverages. The aim of this study was to distinguish differences between DNA and mRNA as template for the detection of this yeast. The study was also used to determine if it is possible to accurately detect cells in the viable but not culturable (VBNC) state of B. bruxellensis by qPCR. Several methods including traditional plating, epifluorescence counts and qPCR were used to amplify DNA and mRNA. It was observed that mRNA was a better template for the detection in terms of standard curve analysis and qPCR efficiencies. Various primers previously published were tested for their specificity, qPCR efficiency and accuracy of enumeration. A single primer set was selected which amplified a region of the actin-encoding gene. The detection limit for this assay was 10cellsmL(-1). B. bruxellensis could also be quantified in naturally contaminated wines with this assay. The mRNA gave a better indication of the viability of the cells which compared favourably to fluorescent microscopy and traditional cell counts. The ability of the assay to accurately estimate the number of cells in the VBNC state was also demonstrated.

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.

Direct Quantitative Detection and Identification of Lactococcal Bacteriophages from Milk and Whey by Real-Time PCR: Application for the Detection of Lactococcal Bacteriophages in Goat's Raw Milk Whey in France

The presence of Lactococcus bacteriophages in milk can partly or completely inhibit milk fermentation. To prevent the problems associated with the bacteriophages, the real-time PCR was developed in this study for direct detection from whey and milk of three main groups of Lactococcus bacteriophages, c2, 936, and P335. The optimization of DNA extraction protocol from complex matrices such as whey and milk was optimized allowed the amplification of PCR without any matrix and nontarget contaminant interference. The real-time PCR program was specific and with the detection limit of 10² PFU/mL. The curve slopes were −3.49, −3.69, and −3.45 with the amplification efficiency estimated at 94%, 94%, and 98% and the correlation coefficient (R²) of 0.999, 0.999, and 0.998 for c2, 936 and P335 group, respectively. This method was then used to detect the bacteriophages in whey and goat's raw milk coming from three farms located in the Rhône-Alpes region (France).

Strategy for the extraction of yeast DNA from artisan agave must for quantitative PCR analysis

An efficient method for the direct extraction of yeast genomic DNA from agave must was developed. The optimized protocol, which was based on silica-adsorption of DNA on microcolumns, included an enzymatic cell wall degradation step followed by prolonged lysis with hot detergent. The resulting extracts were suitable templates for subsequent qPCR assays that quantified mixed yeast populations in artisan Mexican mezcal fermentations.

Saccharomyces cerevisiae vaginitis: microbiology and in vitro antifungal susceptibility

Genitourinary infections by Saccharomyces cerevisiae are rare. Here, we describe eight S. cerevisiae vulvovaginitis episodes where molecular (Affirm VPIII) and conventional microbiological methods (culture and carbohydrate assimilation) have proven to be inadequate for diagnostic purposes. DNA sequencing allowed the correct identification of the pathogen. All isolates were susceptible to most antifungal agents, with two of them also found to be susceptible-dose-dependent to itraconazole.

Development of a sequence-characterized amplified region marker-targeted quantitative PCR assay for strain-specific detection of Oenococcus oeni during wine malolactic fermentation

Control over malolactic fermentation (MLF) is a difficult goal in winemaking and needs rapid methods to monitor Oenococcus oeni malolactic starters (MLS) in a stressful environment such as wine. In this study, we describe a novel quantitative PCR (QPCR) assay enabling the detection of an O. oeni strain during MLF without culturing. O. oeni strain LB221 was used as a model to develop a strain-specific sequence-characterized amplified region (SCAR) marker derived from a discriminatory OPA20-based randomly amplified polymorphic DNA (RAPD) band. The 5' and 3' flanking regions and the copy number of the SCAR marker were characterized using inverse PCR and Southern blotting, respectively. Primer pairs targeting the SCAR sequence enabled strain-specific detection without cross amplification of other O. oeni strains or wine species of lactic acid bacteria (LAB), acetic acid bacteria (AAB), and yeasts. The SCAR-QPCR assay was linear over a range of cell concentrations (7 log units) and detected as few as 2.2 × 10(2) CFU per ml of red wine with good quantification effectiveness, as shown by the correlation of QPCR and plate counting results. Therefore, the cultivation-independent monitoring of a single O. oeni strain in wine based on a SCAR marker represents a rapid and effective strain-specific approach. This strategy can be adopted to develop easy and rapid detection techniques for monitoring the implantation of inoculated O. oeni MLS on the indigenous LAB population, reducing the risk of unsuccessful MLF.

Development and evaluation of a real-time quantitative PCR assay for detection and enumeration of yeasts of public health interest in dairy products

Yeast contamination is a problem in the food industry as a cause of spoilage. Moreover, various species of yeasts are known to be capable of causing opportunistic infections in humans. We have developed a real-time quantitative PCR (qPCR) assay to directly detect and quantify nine emerging opportunistic yeast species (Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, Clavispora lusitaniae, Filobasidiella neoformans, Issatchenkia orientalis, Trichosporon asahii, and Trichosporon jirovecii) in dairy product samples. We designed six primer pairs, conserved sequences of the variable D1/D2 domains of the 26S rRNA gene, to detect the yeasts and demonstrated their specificity. The qPCR assay could accurately quantify emerging opportunistic yeasts in an artificially contaminated dairy product. qPCR with the primer pairs we designed, was very sensitive and will allow producers to enumerate contaminating yeasts and identify whether they are opportunistic pathogens, in only 4 to 5h. This assay can easily be extended to other food items and to a variety of food-monitoring initiatives.

Characterization of the yeast ecosystem in grape must and wine using real-time PCR

The complex microbial ecosystem of grape must and wine harbours a wide diversity of yeast species. Specific oligonucleotide primers for real-time quantitative PCR(QPCR) were designed to analyse several important non-Saccharomyces yeasts (Issatchenkia orientalis, Metschnikowia pulcherrima, Torulaspora delbrueckii, Candida zemplinina and Hanseniaspora spp.) and Saccharomyces spp. in fresh wine must, during fermentation and in the finished wine. The specificity of all primer couples for their target yeast species were validated and the QPCR methods developed were compared with a classic approach of colony identification by RFLP-ITS-PCR on cultured samples. Once the methods had been developed and validated, they were used to study these non-Saccharomyces yeasts in wine samples and to monitor their dynamics throughout the fermentation process. This study confirms the usefulness and the relevance of QPCR for studying non-Saccharomyces yeasts in the complex yeast ecosystem of grape must and wine.