Methods for the rapid detection and identification of yeasts in foods

Isolation and Identification of Yeasts in Marcha, a Rice Wine Starter Culture From Nepal

Nepal harbors a rich diversity of cultures and traditions, including the unique practice of creating an indigenous grain called Marcha by various ethnic groups such as Newar, Tamang, Sherpa, Rai, Limbu, Gurung, Magar, and Tharu people. In the eastern region of Nepal, Marcha producers utilize over 42 different plants, including Vernonia cinerea, Clematis grewiae, Polygala arillata, Buddleja asiatica, Inula sp., Scoparia, and more, which shows regional diversity. The primary objective of the study was to explore the diversity of yeast present in Marcha samples. The studied Marcha samples were collected from 10 different geographic regions of Nepal, which included altogether 27 samples. The isolates were grouped into Groups A, B, and C based on morphological and physiological characteristics. Notably, Group B yeast displayed high amylase production, an enzyme responsible for starch breakdown, and exhibited the ability to produce ethanol. To further investigate the potential of these isolates, stress exclusion tests were conducted, with 30 isolates (70%) showing positive responses. The yeast isolates demonstrated resilience to high glucose concentrations of up to 36% (w/v) at a pH above 3 and a temperature of 37°C, which is the ideal growth condition. The study observed a direct correlation between the yeast isolates' ethanol production capabilities and their tolerance to different ethanol concentrations. Considering that all tested Marcha samples contained yeast capable of starch degradation and ethanol production, it was expected that these yeast isolates would actively participate in the fermentation of starch-based alcohol.

Use of specific PCR primers to identify three important industrial species of Saccharomyces genus: Saccharomyces cerevisiae, Saccharomyces bayanus and Saccharomyces pastorianus

AIM

To develop species-specific primers capable of distinguishing between three important yeast species in alcoholic fermentation: Saccharomyces bayanus, Saccharomyces cerevisiae and Saccharomyces pastorianus.

METHODS AND RESULTS

Two sets of primers with sequences complementary to the HO genes from Saccharomyces sensu stricto species were used. The use of the ScHO primers produced a single amplificon of c. 400 or 300 bp with species S. cerevisiae and S. pastorianus, respectively. The second pair of primers (LgHO) was also constructed, within the HO gene, composed of perfectly conserved sequences common for S. bayanus species, which generate amplicon with 700 bp. No amplification product was observed in the DNA samples from non-Saccharomyces yeasts. Saccharomyces species have also been characterized via electrophoretic karyotyping using pulsed-field gel electrophoresis to demonstrate chromosomal polymorphisms and to determine the evolutionary distances between these species.

CONCLUSIONS

We conclude that our novel species-specific primers could be used to rapidly and accurately identify of the Saccharomyces species most commonly involved in fermentation processes using a PCR-based assay.

SIGNIFICANCE AND IMPACT OF THE STUDY

The method may be used for routine identification of the most common Saccharomyces sensu stricto yeasts involved in industrial fermentation processes in less than 3 h.

Use of molecular methods for the identification of yeast associated with table olives

A molecular approach is used for the identification of yeast isolated from table olives. Our results validate those obtained in the past by the classical biochemical methodology. Yeast were isolated from both aerobically and anaerobically processed black table olives and also from canned seasoned green table olives. Molecular identification methodology used included restriction pattern analysis of both PCR-amplified 5.8S rRNA gene and internal transcribed spacers ITS(1) and ITS(2). For some species, sequence analysis of the 26S rRNA gene was necessary. These techniques allowed the identification of three yeast species (Issatchenkia occidentalis, Geotrichum candidum and Hanseniaspora guilliermondii) which had not been described previously in table olives. Saccharomyces cerevisiae and Candida boidinii were the most frequent species in green seasoned olives and processed black olives, respectively. The molecular study of total DNA variability among the S. cerevisiae strains isolated indicates a quite heterogeneous population, with at least four different restriction patterns.

A real-time PCR assay for the enumeration and detection of Zygosaccharomyces bailii from wine and fruit juices

Zygosaccharomyces bailii is a major food and beverage spoilage organism. Existing methods for its detection involve lengthy enrichment techniques and then the result does not always differentiate between Z. bailii and Saccharomyces cerevisiae. In this work, we developed a quantitative real-time PCR assay for the rapid detection of Z. bailii from fruit juices and wine even in the presence of non-target DNA. Primers were designed to the gene coding for the D1/D2 loop of the 26S ribosomal RNA subunit producing a single PCR product with a melting temperature of 83.5 degrees C. As few as 2 cells per ml could be detected by the assay in cranberry raspberry and apple juices and 22 cells per ml from grape juice. The assay was equally efficient in wine, detecting 6 cells per ml even in the presence of 10(7)S. cerevisiae cells. The CFU/ml as determined by plating on YM media showed excellent correlation with the CFU/ml established by the QPCR assay for all the beverages examined. Unknown samples of Z. bailii were prepared in the juices and wine and examined by QPCR. The QPCR estimated cell number was in good agreement with the cell counts obtained by plating, the exception being the cranberry raspberry juice sample. It was determined by live/dead cell counts that the Z. bailii cells were less viable in this juice thus leading to an overestimation of CFU/ml by QPCR. However, the correlation was high between QPCR and total cell count as determined by fluorescent microscopy. This assay provides a rapid and accurate method to establish the levels of the total Z. bailii population which consists of both viable and nonviable cells.

Detection of Kluyveromyces marxianus and other spoilage yeasts in yoghurt using a PCR-culture technique

A combined PCR-culture technique was developed for the detection of viable yeasts in yoghurt samples. Yoghurt samples were inoculated with either viable or heat-inactivated Kluyveromyces marxianus cells, and analyzed before and after incubation for 24 h at 25 degrees C under agitation. DNA was extracted from the samples and amplified using yeast-specific primers targeted at the gene coding for the 18S rRNA. A 251-bp fragment was amplified by the Polymerase Chain Reaction from the yoghurt samples containing initial yeasts counts of 10 cfu g(-1) or higher, whereas no PCR product was generated from control uninoculated yoghurt samples. Comparison of PCR results obtained before and after the incubation step was used to assess yeast viability. Viability was also confirmed by plating on Sabouraud-Dextrose-Chloramphenicol Agar. Moreover, comparison of the results obtained using PCR-culture and plate count methods for the analysis of commercial yoghurt samples, demonstrated that the PCR-culture technique developed in this work can be very useful for the rapid detection of viable spoilage yeasts in dairy industries.

Molecular detection of Candida krusei contamination in fruit juice using the citrate synthase gene cs1 and a potential role for this gene in the adaptive response to acetic acid

AIMS

To develop a reverse transcription-polymerase chain reaction (RT-PCR) assay to detect viable Candida krusei contaminations and examine the potential role of the citrate synthase (cs1) gene in adaptation to acetic acid.

METHODS AND RESULTS

Fruit juice artificially contaminated with C. krusei cells was heat treated to inactivate the yeast cells, after which the improved ability of the RT-PCR over the PCR assay, through the amplification of the cs1 gene, to differentiate viable contaminations was shown. The sensitivity of the detection assay was 6 x 104 CFU ml-1. RT-PCR and densitometric analysis of the cs1 gene throughout the process of adaptation to acetic acid highlighted a potential role for the gene in the yeast's adaptive response.

CONCLUSIONS

The RT-PCR assay through the targeting of the cs1 gene proved to be a specific, sensitive and direct method for the identification of a C. krusei contamination in a food environment. The cs1 gene was shown to play a potential role in the adaptation of the culture to the weak-acid preservative acetic acid.

SIGNIFICANCE AND IMPORTANCE OF THE STUDY

The development of a direct, sensitive and specific identification assay for C. krusei from a food environment and understanding the mechanism employed in adapting to a preservative challenge, represent important tools to the food industry in attempting to limit spoilage by this important food spoilage yeast.

Molecular characterization of Yarrowia lipolytica and Candida zeylanoides isolated from poultry

Yeast isolates from raw and processed poultry products were characterized using PCR amplification of the internally transcribed spacer (ITS) 5.8S ribosomal DNA region (ITS-PCR), restriction analysis of amplified products, randomly amplified polymorphic DNA (RAPD) analysis, and pulsed-field gel electrophoresis (PFGE). ITS-PCR resulted in single fragments of 350 and 650 bp, respectively, from eight strains of Yarrowia lipolytica and seven strains of Candida zeylanoides. Digestion of amplicons with HinfI and HaeIII produced two fragments of 200 and 150 bp from Y. lipolytica and three fragments of 350, 150, and 100 bp from C. zeylanoides, respectively. Although these fragments showed species-specific patterns and confirmed species identification, characterization did not enable intraspecies typing. Contour-clamped heterogeneous electric field PFGE separated chromosomal DNA of Y. lipolytica into three to five bands, most larger than 2 Mbp, whereas six to eight bands in the range of 750 to 2,200 bp were obtained from C. zeylanoides. Karyotypes of both yeasts showed different polymorphic patterns among strains. RAPD analysis, using enterobacterial repetitive intergenic sequences as primers, discriminated between strains within the same species. Cluster analysis of patterns formed groups that correlated with the source of isolation. For ITS-PCR, extraction of DNA by boiling yeast cells was successfully used.

Polyphasic identification of wild yeast strains isolated from Greek sourdoughs

A total of forty-five wild yeast strains were isolated from five traditional Greek wheat sourdoughs. Strains were identified using the classical identification technique along with the sodium dodecyl sulfate-polyacrylamide gel electrophoresis of whole cell proteins (SDS-PAGE), Fourier transform-infrared spectroscopy (FT-IR) and the randomly amplified polymorphic DNA-polymerase chain reaction analysis (RAPD-PCR). The latter methods confirmed the classical identification. According to the results obtained, fourteen strains were identified as Saccharomyces cerevisiae strains, twenty-five as Pichia membranaefaciens strains and six as Yarrowia lipolytica.

Molecular taxonomy of yeasts

In the last two decades the application of molecular techniques has had a major impact on the classification of yeasts. The nuclear DNA relatedness has become the basis of species delineation. Molecular fingerprinting methods such as analysis of restriction fragment length polymorphisms, random amplified polymorphic DNA, PCR-amplified sequences and fragments, pulsed field gel electrophoresis of chromosome DNA and others allow intraspecies differentiation and typing. The most far reaching method has been the sequencing of various parts of ribosomal DNA that has made for the first time possible to assess the phylogenetic relationships among yeasts at different taxonomic levels. Based on the molecular data obtained so far several changes have been introduced in the classification of yeasts, however, substantial restructuring of current taxonomic schemes with the consequence of numerous nomenclatural changes must await further studies.