Differentiation of contaminating yeasts in brewery by PCR-based techniques

Tetrad analysis of sake yeast and identification of an RFLP marker for the absence of phenolic off-flavour production

Mating is a promising breeding method for industrial yeast. Although sake yeast has a low spore-formation ability, segregants exhibiting a mating type have been isolated from sake yeast K7. Here, we constructed zygotes from a cross between those segregants and a laboratory yeast strain. Because most sake and brewing yeast strains are prototrophs, we developed a PCR-based method to confirm that mating had taken place based on genome sequencing data and differences in nucleotide sequences between the two parental strains. The mated strain, termed S. cerevisiae MITOY123, showed restored spore-formation ability, unlike most sake and brewing yeast strains. By using the mated yeast strain MITOY123, it was possible to carry out tetrad analysis for the trait of the absence of off-flavour due to phenolic products such as 4-vinylguiacol (4-VG) in sake yeast K7. This tetrad analysis indicated that a single genetic region around the gene PAD1 is responsible for the absence of phenolic off-flavour in sake yeast K7. In order to aid the breeding of sake and brewing yeast strains by mating, we also identified a restriction fragment length polymorphism (RFLP) marker for the absence of phenolic off-flavour production in strains derived from sake yeast K7. Collectively, our data show that it is possible to breed new sake and brewing yeast strains by mating and to test for the absence of phenolic off-flavour production in resultant strains easily by RFLP analysis.

In Vitro Probiotic Properties and DNA Protection Activity of Yeast and Lactic Acid Bacteria Isolated from A Honey-Based Kefir Beverage

The probiotic characteristics of three acid-tolerant microbial strains, viz.,Lactobacillus satsumensis LPBF1, Leuconostoc mesenteroides LPBF2 and Saccharomyes cerevisiae LPBF3, isolated from a honey-based kefir functional beverage, were studied following the requirements established by the Food and Agriculture Organization of the United Nation/World Health Organization (FAO/WHO), including host-associated stress resistance, epithelium adhesion ability, and antimicrobial activity. The three microbial strains tolerated different pH values (2.0, 3.0, 4.0 and 7.0) and bile salt concentrations (0.3% and 0.6%), and survive in the presence of simulated gastric juice, which are conditions imposed by the gastrointestinal tract. In addition, they showed high percentages of hydrophobicity, auto aggregation and anti-pathogenic against Escherichia coli and Staphylococcus aureus, with no hemolytic activity. The protective capacity of human DNA through microbial treatment was investigated by single-cell gel electrophoresis (SCGE) comet assay. The three selected strains showed DNA protection effect against damage caused by hydroxyl radical (H₂O₂). However, when the S. cerevisiae treatment was applied, the most effective DNA protection index was observed, which can be associated to its high production of extracellular antioxidants as reveled by the 2,2-diphenyl-1-picryl-hydrazylhydrate (DPPH) method. These results indicated that the three selected microbial strains could be useful for preventing oxidative DNA damage and cellular oxidation in food products. As well-adapted microbial cells, the selected strains can be used for production of non-dairy functional beverages, especially for vegans and/or vegetarians and lactose intolerants.

Isolation, selection and evaluation of antagonistic yeasts and lactic acid bacteria against ochratoxigenic fungus Aspergillus westerdijkiae on coffee beans

In this study, yeasts and lactic acid bacteria (LAB) were isolated from coffee fruits and identified via biochemical and molecular approaches. The isolates represented the Pichia, Debaryomyces, Candida, Clavispora, Yarrowia, Sporobolomyces, Klyveromyces, Torulaspora and Lactobacillus genera. Four isolates, namely Pichia fermentans LPBYB13, Sporobolomyces roseus LPBY7E, Candida sp. LPBY11B and Lactobacillus brevis LPBB03, were found to have the greatest antagonist activity against an ochratoxigenic strain of Aspergillus westerdijkiae on agar tests and were selected for further characterization. Applications of P. fermentans LPBYB13 in coffee cherries artificially contaminated with A. westerdijkiae showed efficacy in reducing ochratoxin A (OTA) content up to 88%. These results highlight that P. fermentans LPBYB13 fulfils the principle requirements of an efficient biological control of aflatoxigenic fungi in coffee beans and may be seen as a reliable candidate for further validation in field conditions.

SIGNIFICANCE AND IMPACT OF THE STUDY

Studies based on microbial ecology and antagonistic interactions are important for the development of new strategies in controlling aflatoxin contamination of crops and are relevant to further biotechnological applications. This study shows that coffee fruit is a potential source for the isolation of microbial strains with antifungal ability. A new yeast strain, Pichia fermentans LPBYB13, showed efficacy in reducing growth and ochratoxin A production of Aspergillus westerdijkiae in coffee beans. Our results should encourage the use of this yeast strain on a large scale for biocontrol of aflatoxigenic fungi in coffee beans.

Evaluation of ITS PCR and RFLP for Differentiation and Identification of Brewing Yeast and Brewery 'Wild' Yeast Contaminants

A reference library of ITS PCR/RFLP profiles was collated and augmented to evaluate its potential for routine identification of domestic brewing yeast and known ‘wild’ yeast contaminants associated with wort, beer and brewing processes. This library contains information on band sizes generated by restriction digestion of the ribosomal RNA‐encoding DNA (rDNA) internal transcribed spacer (ITS) region consisting of the 5.8 rRNA gene and two flanking regions (ITS1 and ITS2) with the endonucleases CfoI, HaeIII, HinfI and includes strains from 39 non‐Saccharomyces yeast species as well as for brewing and non‐brewing strains of Saccharomyces. The efficacy of the technique was assessed by isolation of 59 wild yeasts from industrial fermentation vessels and conditioning tanks and by matching their ITS amplicon sizes and RFLP profiles with those of the constructed library. Five separate, non‐introduced yeast taxa were putatively identified. These included Pichia species, which were associated with conditioning tanks and Saccharomyces species isolated from fermentation vessels. Strains of the lager yeast S. pastorianus could be reliably identified as belonging to either the Saaz or Frohberg hybrid group by restriction digestion of the ITS amplicon with the enzyme HaeIII. Frohberg group strains could be further sub‐grouped depending on restriction profiles generated with HinfI.

RAPD with microsatellite as a tool for differentiation of Candida genus yeasts isolated in brewing

Fifteen wild yeast strains were isolated in two factories of a lager brewing company in Poland. Their identification with API 32C system showed mainly the presence of Candida sake species (7/15). To differentiate the isolates, randomly amplified polymorphic DNA (RAPD) with (GTG)(5), (GAC)(5), (GACA)(4) microsatellite primers and M13 core sequence (5'-GAG GGT GGC GGT TCT-3') were chosen. The results of patterns similarity are presented as dendrograms for each RAPD analysis and for overall patterns. On the overall patterns, all isolates identified as C. sake, except Strain No. 1, were regrouped in one cluster. Collection strain C. sake CBS 617 was similar in 46% to the cluster with six isolates (Strain Nos. 3, 6, 8, 11, 13, 14). The second reference strain C. sake CBS 159 and the Strain No. 1 were regrouped with other Candida species (collection strains) showing, respectively, only 20% and 42% of similarity to other C. sake strains. The similarity based on the overall dendrogram between isolate Nos. 3, 6, 8, 11, 13, 14 and C. sake CBS 617 was 49%. Between those strains and other Candida, the similarity was only 37%.

Potential application of ribosomal intergenic spacer analysis to the microbial community analysis of agronomic products

Ribosomal intergenic spacer analysis (RISA) has been applied to the microbial community analysis of agronomic products in combination with a simple and rapid DNA extraction method, consisting of a one-step extraction and two-step purification, for a variety of agronomic products. RISA appears to be a useful tool for the study of the community structures of food-associated microbes and their use as a unique fingerprinting signature for each agronomic product. Sequencing analyses of amplicons generated from RISA suggest that this method can detect conventional microbes. In the case of RISA of wasabi paste DNA, the sequences of the amplicons showed high similarity to the plant pathogen Xanthomonas campestris and the soil bacterium Bacillus subtilis, whereas several food-associated bacteria (Lactococcus lactis, Lactococcus raffinolactis, and Lactococcus sakei) were detected using this technique in sausage DNA. Unexpectedly, the sequencing analyses also revealed the presence of several microbes that possessed high similarity to human bacterial pathogens such as Weissella confusa and Yersinia pestis. The results suggest that RISA will be a useful method for routine microbial community analysis in agronomic products.

Enological and genetic traits of Saccharomyces cerevisiae isolated from former and modern wineries

Saccharomyces cerevisiae strains isolated from two different wineries in central Italy were subjected to enological and molecular characterization to investigate the influence of the winery environment. One of the selected wineries is a modern, working winery, whereas the second one was abandoned since 1914 and was located in an artificial cavern. The results obtained by our analysis of the fermentation traits underline the selectivity of the winery environment (winery effect), since strains isolated from the industrial winery showed higher values for characters typically subjected to selective pressure, such as maximum capability to produce ethanol, fermentation rate and SO(2) resistance. Pulsed-field gel electrophoresis (PFGE), random amplification of polymorphic DNA (RAPD)-PCR and SAU-PCR were carried out to assesss genetic differences between the two populations studied. Only RAPD-PCR could distinguish between the two populations based on their provenience, whereas PFGE and SAU-PCR gave profiles shared between strains isolated from the industrial and former winery. Moreover, analysis of the karyotypes suggested the presence of chromosomal-length polymorphism; differences in the size and number of chromosomes between the two groups of isolates, as well as within each group, were observed.