Yeast dynamics during the fermentation of brined green olives treated in the field with kaolin and Bordeaux mixture to control the olive fruit fly

The yeast microbiota associated with naturally fermented and inoculated green table olives, differently treated in the field with non-conventional repellent and antiovipositional products in the control of Bactrocera oleae, was analysed using a combination of culture-dependent and -independent molecular fingerprinting. The routine yeast isolation gave rise to 118 strains, whose identification was performed by PCR-RFLP of the internal transcribed spacer (ITS) regions. Total DNA was extracted directly from the brine throughout fermentation by means of an experimental protocol that included the removal of Taq polymerase inhibitors. Denaturing Gradient Gel Electrophoresis (DGGE) of 26S rRNA gene PCR amplicons highlighted the yeast community. Comparison of both culture-dependent and independent methods indicated that the yeast species Saccharomyces cerevisiae, Wickerhamomyces anomalus, Candida diddensiae and Issatchenkia orientalis were dominant during fermentation despite the addition of the Lactobacillus plantarum starter used in brining. The resultant isolated species were unaffected by treatments in field, except for C. diddensiae whose growth was delayed by kaolin.     

A PCR-TGGE (Temperature Gradient Gel Electrophoresis) technique to assess differentiation among enological Saccharomyces cerevisiae strains

In this paper new primers, annealing to the ITS2 region, were used to obtain a PCR product that was subsequently subjected to Temperature Gradient Gel Electrophoresis (TGGE) analysis. The PCR-TGGE method performed was able to distinguish Saccharomyces cerevisiae and S. paradoxus and distinguish between strains of S. cerevisiae. Direct analysis of S. cerevisiae and S. paradoxus ecology in musts were also performed.     

Lactic acid bacteria ecology of three traditional fermented sausages produced in the North of Italy as determined by molecular methods

In this study the bacterial biodiversity during the maturation process of three traditional sausages produced in the North of Italy (Salame bergamasco, Salame cremonese and Salame mantovano) was investigated by using culture-dependent and -independent methods. Eleven plants, in the three provinces considered here, were selected because starter cultures were never used in the production. The bacterial ecology, as determined by plate counts, was dominated by lactic acid bacteria (LAB), with minor contribution of coagulase negative cocci and yeasts. After molecular identification of 486 LAB strains, the species more frequently isolated were Lactobacillus sakei and Lactobacillus curvatus. This evidence was also confirmed by PCR-Denaturing Gradient Gel Electrophoresis (DGGE). All the samples analyzed were characterized by the constant presence of L. sakei and L. curvatus bands. A richer biodiversity was only detected at the beginning of maturation. The results obtained by the molecular characterization of the L. sakei and L. curvatus and by the cluster analysis of the DGGE profiles highlighted a plant-specific population, rather than a geographic characterization of the products, underlining how the environmental and processing conditions are able to select specific microbiota responsible for the main transformations during the fermentation and ripening of the sausages.     

Culture-dependent and culture-independent qualitative analysis of probiotic products claimed to contain bifidobacteria

A total of 58 probiotic products obtained worldwide, which were claimed to contain Bifidobacterium strains (including 22 yoghurts, 5 dairy fruit drinks, 28 food supplements and 3 pharmaceutical preparations) were investigated in parallel using a culture-dependent and a culture-independent approach. Three isolation media previously reported as selective for Bifidobacterium were evaluated for their suitability in the quality analysis of these products. Subsequently, possible bifidobacterial colonies were picked from the best medium and identified by means of rep-PCR fingerprinting using the BOX primer (BOX-PCR). Bifidobacterium animalis subsp. lactis, formerly classified as Bifidobacterium lactis, was most frequently found, but strains belonging to Bifidobacterium longum biotypes longum and infantis, Bifidobacterium bifidum and Bifidobacterium breve were recovered also. In parallel, all products were also subjected to culture-independent analysis which involved a nested-PCR step on total bacterial DNA extracted directly from the product, followed by separation of the amplicons by Denaturing Gradient Gel Electrophoresis (DGGE) and subsequent identification of species from the band patterns. By conventional cultivation, 70.7% of the products analysed were found to contain culturable bifidobacteria whereas by culture-independent DGGE analysis members of the genus Bifidobacterium could be detected in 96.5% of the analysed products. Genotypic characterization of a number of bifidobacterial isolates at the strain level by means of Pulsed-Field Gel Electrophoresis (PFGE) revealed a relatively high degree of genomic homogeneity among the Bifidobacterium strains currently used in the probiotic industry.     

PCR‐TTGE and RAPD‐PCR Techniques to Analyze Saccharomyces cerevisiae and Saccharomyces carlsbergensis Isolated from Craft Beers

In the Friuli Venezia Giulia region (North East of Italy) the production of craft beers has been increasing constantly. Usually microbreweries use yeasts supplied by Italian or foreign industrial breweries for beer production. Yeast species are often not known, moreover the vitality, the viability, the physiological state and the number of generation are not known. To improve the quality of the final product it is important to evaluate the quality of the yeast strain used and the lactic acid bacteria contamination. Various molecular methods have been developed to compare genetic characteristics of yeast strains used in beer and wine production. The methods proposed in this work, PCR‐TTGE and RAPD‐PCR techniques, allow the comparison of specific DNA sequences to identify and/or characterize yeast strains. The molecular methods are faster than traditional methods and they allowed the identification of the strains analysed as S. cerevisiae and the intraspecies differentiation among yeast strains tested within 8 h after cell growth.     

Microbiological and Fermentative Properties of Baker's Yeast Starter Used in Breadmaking

This study assessed the levels of microbial contaminants in liquid, compressed and dry commercial baker's yeasts used as starters in breadmaking. Eumycetes, Enterobacteriaceae, total and fecal coliforms, Bacillus spp., and lactic acid bacteria (LAB), in particular enterococci, were quantified. Results obtained in this study highlighted that baker's yeast could represent a potential vehicle of spoilage and undesirable microorganisms into the baking environment, even if these do not influence the leavening activity in the dough, as ascertained by rheofermentometer analysis. Different microbial groups, such as spore‐forming bacteria and moulds, were found in baker's yeast starters. Moreover, different species of LAB, which are considered the main contaminants in large‐scale yeast fermentations, were isolated and identified by Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rDNA sequencing. The most recurrent species were Lactobacillus plantarum, Enterococcus faecalis, and Enterococcus durans, isolated from both compressed and dry starters, whereas strains belonging to Leuconostoc and Pediococcus genera were found only in dry ones. Nested‐Polymerase Chain Reaction (Nested‐PCR) and Randomly Amplified Polymorphic DNA–PCR (RAPD‐PCR) were also used to highlight the biodiversity of the different commercial yeast strains, and to ascertain the culture purity.     

Use of PCR‐DHPLC (Polymerase Chain Reaction—Denaturing High Performance Liquid Chromatography) for the Rapid Differentiation of Industrial Saccharomyces pastorianus and Saccharomyces cerevisiae Strains

Strain specific detection and control of Saccharomyces pastorianus and Saccharomyces cerevisiae starter cultures is of great importance for the fermentation industry. The preconditions of strain specific fermentation characteristics can be ensured by periodic analysis and confirmation of the strain identity. With regard to industrial S. pastorianus and S. cerevisiae strains and a focus on brewing strains, the differentiation methods most available are time‐consuming and not very discriminative. In this work PCR‐DHPLC analysis was investigated as a novel approach for the differentiation of industrially used S. pastorianus and S. cerevisiae strains. The PCR‐DHPLC‐system was specific for S. cerevisiae strains and S. pastorianus hybrid strains that contain IGS2 rDNA, which originates from the S. cerevisiae ancestor. For the DNA of 177 strains of 41 non‐target species, which are typical for beverage and fermentation surroundings, the absence of PCR‐amplificates could be confirmed by DHPLC analysis. It was shown that single strains of S. cerevisiae and S. pastorianus could be differentiated. A strain specific differentiation within the group of top‐fermenting Saccharomyces cerevisiae strains could also be performed. For the group of bottom fermenting S. pastorianus brewing strains, strain‐to‐strain specific differences in the DHPLC chromatograms could be observed which can be used to differentiate and to compare two single strains with each other, although the comparison of chromatograms of an unknown S. pastorianus strain with a set of known S. pastorianus chromatograms could only reveal tendencies towards grouping into types. The differential DHPLC chromatogram characteristics (fluorescence intensities, number of peaks/side‐peaks/peak‐shoulders) within S. pastorianus are present, but not as distinctive as for S. cerevisiae. Additionally PCR‐DHPLC has advantages compared to other differentiation methods, such as species specificity, speed (2.5 h for one sample) and precision with the described limits.     

Microflora of Feta cheese from four Greek manufacturers

The components of the microflora of four Feta cheeses, produced by different Greek manufacturers, were determined by culture dependent and independent techniques. Isolates from microbiological media were first grouped by Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and then representatives of each DGGE group were sequenced for identification purposes. DNA and RNA, extracted directly from the cheese, were subjected to PCR-DGGE. Moreover, Feta cheeses were subjected to FISH analysis in order to identify viable bacterial populations. The microbial ecology, as represented by the Lactic Acid Bacteria (LAB) and yeast populations, was different for the four cheeses. The main LAB species isolated were Lactobacillus plantarum, Lactobacillus brevis, Lactobacillus coryniformis and Lactobacillus fermentum. However, some inconsistencies were observed between the results obtained with the culture dependent and the culture independent approach. In the case of the yeasts, the results obtained by PCR-DGGE compared very well with those obtained by the conventional microbiological analysis and the main species found were Kluyveromyces lactis, Pichia fermentans and C. zeylanoides. FISH analysis highlighted viable but not culturable populations of Streptococcus thermophilus and Lactococcus spp. RAPD-PCR performed on the L. plantarum isolates revealed a cheese specific distribution and a temperature dependent clustering.     

A RAPID,SIMPLE AND RELIABLE METHOD OF DIFFERENTIATING BREWING YEAST STRAINS BASED ON DNA RESTRICTION PATTERNS

DNA was isolated from polyploid brewing ale and lager yeast strains using a simple and rapid procedure which was a modification of a previously described method of Seehaus et al.¹⁴ The isolated DNA was cut with a number of restriction enzymes and subjected to agarose gel electrophoresis. Significant differences in banding patterns were observed between a Saccharomyces cerevisiae ale strain DNA and Saccharomyces uvarum (carlsbergensis) lager strain DNA, particularly with the enzyme Hpal. Differences were also observed between the banding patterns of digests from two ale strains, and from two lager strains. Use of this technique with appropriate restriction enzymes should prove useful for the rapid differentiation of brewing yeast strains.     

自然发酵乳中粪肠球菌和屎肠球菌的4种鉴定方法的比较

采用传统生理生化鉴定方法,16S rRNA基因序列分析技术,16S-23S rRNA间区序列多态性分析技术,变性梯度凝胶电泳技术(DGGE),对分离于自然发酵乳中的9株粪肠球菌和6株屎肠球菌进行鉴定,并对4种鉴定方法进行比较和评价。结果表明,16S-23S rRNA间区序列多态性分析技术和DGGE技术不但可以快速、精确地区分粪肠球菌和屎肠球菌,而且能够将粪肠球菌和屎肠球菌种内的不同基因亚型区分开,而传统生理生化鉴定方法和16S rRNA基因序列分析技术较以上两种方法区分效果略差。     

Investigation of Microbial Communities of Chinese Sourdoughs Using Culture‐Dependent and DGGE Approaches

Sourdough is typically characterized by the complex microbial communities mainly comprising of yeasts and lactic acid bacteria (LAB). The objective of this study was to explore the microbiota of Chinese traditional sourdoughs collected from different areas of China using culture‐dependent and denaturing gradient gel electrophoresis (DGGE) methods. A total of 131 yeasts, 2 molds, and 106 LAB strains were isolated and identified. Based on the culture‐dependent analysis, the populations of yeasts and LAB were at the level of 10⁵ to 10⁷ and 10⁶ to 10⁷ cfu/g, respectively. Similarly, the results of RT‐qPCR showed that the values of total yeasts and LAB populations were in the range of 10⁶ to 10⁷ and 10⁷ to 10⁸ copies/g, respectively. Using culture‐dependent method, a total of 7 yeasts, 2 molds and 7 LAB species were identified. Results showed that Saccharomyces cerevisiae and Lactobacillus plantarum were the predominant species among the yeasts and LAB microflora. Similarly, using PCR‐DGGE approach, 7 yeasts, 1 mold and 9 LAB species were detected. The yeast, S. cerevisiae, represented the predominant, while the yeast Candida tropicalis represented the subdominant species of the yeast community. Among the LAB community, Lactobacillus sanfranciscensis was the predominant species, while Lactococcus qarvieae, Enterococcus faecium, Lactobacillus delbrueckii and Enterococcus cecorum were among the less dominant species.     

Application of culture culture-independent molecular biology based methods to evaluate acetic acid bacteria diversity during vinegar processing

Acetic acid bacteria (AAB) are considered fastidious microorganisms because they are difficult to isolate and cultivate. Different molecular approaches were taken to detect AAB diversity, independently of their capacity to grow in culture media. Those methods were tested in samples that originated during traditional vinegar production. Bacterial diversity was assessed by analysis of 16S rRNA gene, obtained by PCR amplifications of DNA extracted directly from the acetification container. Bacterial composition was analyzed by RFLP-PCR of 16S rRNA gene, Temporal Temperature Gradient Gel Electrophoresis (TTGE) separation of amplicons containing region V3-V5 of 16S rRNA gene and cloning of those amplicons. TTGE bands and clones were grouped based on their electrophoretic pattern similarity and sequenced to be compared with reference strains. The main microorganism identified in vinegar was Acetobacter pasteurianus, which at the end of the acetification process was considered to be the only microorganism present. The diversity was the highest at 2% acetic acid, where indefinite species of Gluconacetobacter xylinus/europaeus/intermedius were also present.     

Methods for yeast characterization from industrial products

This work compared the efficiency of four methods for the identification of industrial yeast strains and the establishment of a pattern for yeast characterization to be used during industrial fermentation processes, allowing the detection of yeast contaminants. Five strains of yeast currently used in the Brazilian fuel alcohol industry (about 99% of the yeast used for this purpose), and yeast strains isolated from the five major beer industries that represent 95% of the Brazilian beer market were evaluated for their growth and absorption of dyes on differential culture media, their total protein electrophoretic patterns (SDS–PAGE), CHEF chromosome separation patterns, and RAPD profiles. For the identification of brewing yeast, all tested methods were efficient, allowing the identification of at least two different species, one of which wasSaccharomyces cerevisiae . The strains used for the fuel alcohol industries were best characterized by SDS–PAGE and RAPD analysis. Those strains share high level of genetic similarity and they are all known as S. cerevisiae strains.     

Diversity of lactic acid bacteria population in ripened Parmigiano Reggiano cheese

The diversity of dominant lactic acid bacteria population in 12 months ripened Parmigiano Reggiano cheeses was investigated by a polyphasic approach including culture-dependent and independent methods. Traditional plating, isolation of LAB and identification by 16S rDNA analysis showed that strains belonging to Lactobacillus casei group were the most frequently isolated. Lactobacillus helveticus, Lactobacillus delbrueckii subsp. lactis, Lactobacillus parabuchneri, and Lactobacillus buchneri species were detected with lower frequency. PCR-denaturing gradient gel electrophoresis (DGGE) applied to DNA extracted directly from cheese samples and sequencing of rDNA amplicons confirmed the complex microbiological pattern of LAB in ripened Parmigiano Reggiano cheeses, with the significant exception of the Lactobacillus fermentum species, which dominated in several samples, but was not detected by cultivation. The present combination of different approaches can effectively describe the lactic acid bacteria population of Parmigiano Reggiano cheese in advanced stages of ripening, giving useful information for elucidating the role of LAB in determining the final cheese quality.     

发酵乳活性双歧杆菌种类快速识别及定量研究

本文建立了发酵乳制品中双歧杆菌种类和数量快速测定方法。以发酵乳中双歧杆菌为靶标,采用PCR-DGGE技术快速识别双歧杆菌种类;采用Real-Tine PCR手段测定双歧杆菌数量。研究结果表明,PCR-DGGE能准确、快速鉴别双歧杆菌种类,检出限为105 CFU/g;Real-Tine PCR能准确、快速定量双歧杆菌,检出限为104 CFU/g。该方法可用于发酵乳中双歧杆菌的快速识别和定量。     

The Production of Isoamyl Acetate from Amyl Alcohol by Saccharomyces cerevisiae

Isoamyl acetate is a natural flavour ester, widely used as a source of banana flavour by the food industry. Fusel alcohols such as amyl alcohol are produced in significant quantities as a waste product, sometimes referred to as “lees oil” or “fusel oil”, of the alcohol distilling industry. By manipulation of brewing yeast fermentation conditions, a significant portion of added amyl alcohol was shown to be converted to isoamyl acetate. This was achieved by the addition of L‐leucine and amyl alcohol in fermentations carried out by a high ester‐producing brewing yeast strain of Saccharomyces cerevisiae and by the use of alkaline fermentation conditions coupled with high gravity media. Mutant strains selected on 5,5,5 trifluoro‐DL‐leucine produced substantially high levels of isoamyl acetate. The adjustment of fermentation conditions outlined in this paper may act as a stepping stone for the potential use of Saccharomyces cerevisiae and other yeasts to produce high levels of natural flavour esters.     

CHARACTERIZATION OF BREWING YEAST STRAINS BY NUMERICAL ANALYSIS OF TOTAL SOLUBLE CELL PROTEIN PATTERNS

Total soluble cell proteins from 33 yeast strains from the brewing industry were extracted and subjected to polyacrylamide gel electrophoresis. Yeast strains were grouped by computerized numerical analysis of protein banding patterns. Three clusters were obtained at r>0.90. Cluster I contained 21 Saccharomyces cerevisiae lager beer strains. Cluster II comprised two strains isolated from beer with a phenolic off flavour and a third strain used for lager beer brewing. Cluster III consisted of two bottom ale yeasts. Protein patterns of yeast strains within each cluster corresponded closely or were identical. However, the intensity of certain bands often varied and the number of peaks recorded was not identical. These minor differences were reproducible and regarded as characteristic for the specific strains. Protein patterns can therefore be used to characterize or fingerprint individual yeast strains.     

Designed construction of recombinant DNA at the ura3Δ0 locus in the yeast Saccharomyces cerevisiae

Recombinant DNAs are traditionally constructed using Escherichia coli plasmids. In the yeast Saccharomyces cerevisiae, chromosomal gene targeting is a common technique, implying that the yeast homologous recombination system could be applied for recombinant DNA construction. In an attempt to use a S. cerevisiae chromosome for recombinant DNA construction, we selected the single ura3Δ0 locus as a gene targeting site. By selecting this single locus, repeated recombination using the surrounding URA3 sequences can be performed. The recombination system described here has several advantages over the conventional plasmid system, as it provides a method to confirm the selection of correct recombinants because transformation of the same locus replaces the pre‐existing selection marker, resulting in the loss of the marker in successful recombinations. In addition, the constructed strains can serve as both PCR templates and hosts for preparing subsequent recombinant strains. Using this method, several yeast strains that contained selection markers, promoters, terminators and target genes at the ura3Δ0 locus were successfully generated. The system described here can potentially be applied for the construction of any recombinant DNA without the requirement for manipulations in E. coli. Interestingly, we unexpectedly found that several G/C‐rich sequences used for fusion PCR lowered gene expression when located adjacent to the start codon. Copyright © 2013 John Wiley & Sons, Ltd.