Selective media for detecting and enumerating foodborne yeasts

Hannaella oleicumulans sp. nov. and Hannaella higashiohmiensis sp. nov., two novel oleaginous basidiomycetous yeast species

Three strains of novel oleaginous yeast species were isolated from soil samples collected in Shiga Prefecture, Japan. The sequences of the internal transcribed spacer (ITS) region and the D1/D2 region of the large subunit (LSU) of the rRNA genes indicated that these novel yeast species are members of the genus Hannaella. The results of molecular phylogenetic analysis indicated that strains 38-3 and 8s1 were closely related to Hannaella oryzae. They differed by 10 nucleotide substitutions and one gap (1.77 %) in the D1/D2 region of the LSU of the rRNA genes and by 17-18 nucleotide substitutions and 10-11 gaps (5.45-5.85 %) in the ITS region. Strain 51-4 differed from the type strain of the most closely related species, Hannaella pagnoccae, by 26 nucleotide substitutions (4.46 %) in the D1/D2 region of the LSU of the rRNA genes and by 20 nucleotide substitutions and six gaps (5.42 %) in the ITS region. The names proposed for these previously undescribed species are Hannaella oleicumulans sp. nov. and Hannaella higashiohmiensis sp. nov.

A study on rheological properties, sensory evaluation and shelf life of ayran-shalgam mixtures

Ayran, a dairy-based fermented beverage, and shalgam, a plant-based fermented beverage were mixed [25% ayran + 75% shalgam (v/v), 50% ayran + 50% shalgam (v/v) and 75% ayran + 25% shalgam (v/v)] and rheological data were obtained at different temperature levels (4-12 °C). Power law model was used to describe the data. Temperature had no effect on the flow behavior index, but it affected the consistency index of the mixtures. Ayran-shalgam mixtures had similar flow behavior index with that of shalgam irrespective of the levels of ayran or shalgam. However, consistency index increased as the amount of ayran increased in the mixtures at a constant temperature. Mixture with the higher amount of ayran [75% ayran + 25% shalgam] had the highest scores in sensory evaluation. Shelf life analyses up to 4 weeks at 4 °C indicated that serum separation increased till the second week and then stabilized for all mixtures. Slight increase (0.05-0.1 unit) in pH was observed during the first week then pH values were stabilized just like the serum separation. Microbiological analyses revealed that mixtures had a similar shelf life with that of ayran. Consequently, mixture of two different fermented beverages could be possible with similar flow behavior and shelf-life, and ayran-shalgam mixture has a huge potential for commercial production. This study may be a basis for designing new products to fulfill the healthy diet demands.

Spare and repair the gut microbiota from antibiotic-induced dysbiosis: state-of-the-art

Homeostasis of the intestinal microbiota is currently recognized as a major contributor to human health. Furthermore, intestinal dysbiosis is associated with a multitude of consequences, including intestinal colonization by antibiotic-resistant or pathogenic bacteria, such as Clostridioides difficile, and reduced efficacy of promising anticancer immunotherapies. By far, the most immediate and drastic exposure leading to dysbiosis is antibiotic treatment. Many attempts have been made to prevent or repair antibiotic-associated dysbiosis. Here, we review these innovations and the difficulties associated with their development.

Optimum cold plasma generating device for treatment of Aspergillus flavus from nuts surface

The objective of this research is to avail an optimum cold plasma generating device for inactivating Aspergillus flavus from nuts surface. For this purpose, a variety of tests were carried out using three applicable plasma generating devices such as atmospheric pressure capacitive coupled plasma (AP-CCP), direct current diode plasma (DC-DP), and inductively coupled plasma (ICP) for different values of input power, pressure, and irradiation time, using Argon gas. The experimental results were achieved upon performing irradiation of sample pistachio nuts by the aforementioned three devices. Finally, after data analysis based on two factors of toxin inactivation amount and cost feasibility for large scale industrial applications, the AP-CCP device was found to be as an optimum device with an acceptable 4 Logs fungi reduction. However, on the basis of single factor, i.e. toxin reduction rate, the DC-DP device works better with a highest fungi reduction rate of 5 Logs, using Argon in 1 Torr vacuum pressure, 300 W and 20 min irradiation.

Kombucha: a novel model system for cooperation and conflict in a complex multi-species microbial ecosystem

Kombucha, a fermented tea beverage with an acidic and effervescent taste, is composed of a multispecies microbial ecosystem with complex interactions that are characterized by both cooperation and conflict. In kombucha, a complex community of bacteria and yeast initiates the fermentation of a starter tea (usually black or green tea with sugar), producing a biofilm that covers the liquid over several weeks. This happens through several fermentative phases that are characterized by cooperation and competition among the microbes within the kombucha solution. Yeast produce invertase as a public good that enables both yeast and bacteria to metabolize sugars. Bacteria produce a surface biofilm which may act as a public good providing protection from invaders, storage for resources, and greater access to oxygen for microbes embedded within it. The ethanol and acid produced during the fermentative process (by yeast and bacteria, respectively) may also help to protect the system from invasion by microbial competitors from the environment. Thus, kombucha can serve as a model system for addressing important questions about the evolution of cooperation and conflict in diverse multispecies systems. Further, it has the potential to be artificially selected to specialize it for particular human uses, including the development of antimicrobial ecosystems and novel materials. Finally, kombucha is easily-propagated, non-toxic, and inexpensive, making it an excellent system for scientific inquiry and citizen science.

LAMP-based group specific detection of aflatoxin producers within Aspergillus section Flavi in food raw materials, spices, and dried fruit using neutral red for visible-light signal detection

Aflatoxins can be produced by 21 species within sections Flavi (16 species), Ochraceorosei (2), and Nidulantes (3) of the fungal genus Aspergillus. They pose risks to human and animal health due to high toxicity and carcinogenicity. Detecting aflatoxin producers can help to assess toxicological risks associated with contaminated commodities. Species specific molecular assays (PCR and LAMP) are available for detection of major producers, but fail to detect species of minor importance. To enable rapid and sensitive detection of several aflatoxin producing species in a single analysis, a nor1 gene-specific LAMP assay was developed. Specificity testing showed that among 128 fungal species from 28 genera, 15 aflatoxigenic species in section Flavi were detected, including synonyms of A. flavus and A. parasiticus. No cross reactions were found with other tested species. The detection limit of the assay was 9.03pg of A. parasiticus genomic DNA per reaction. Visual detection of positive LAMP reactions under daylight conditions was facilitated using neutral red to allow unambiguous distinction between positive and negative assay results. Application of the assay to the detection of A. parasiticus conidia revealed a detection limit of 211 conidia per reaction after minimal sample preparation. The usefulness of the assay was demonstrated in the analysis of aflatoxinogenic species in samples of rice, nuts, raisins, dried figs, as well as powdered spices. Comparison of LAMP results with presence/absence of aflatoxins and aflatoxin producing fungi in 50 rice samples showed good correlation between these parameters. Our study suggests that the developed LAMP assay is a rapid, sensitive and user-friendly tool for surveillance and quality control in our food industry.

Repertory of eukaryotes (eukaryome) in the human gastrointestinal tract: taxonomy and detection methods

Eukaryotes are an important component of the human gut, and their relationship with the human host varies from parasitic to commensal. Understanding the diversity of human intestinal eukaryotes has important significance for human health. In the past few decades, most of the multitudes of techniques that are involved in the diagnosis of the eukaryotic population in the human intestinal tract were confined to pathological and parasitological aspects that mainly rely on traditionally based methods. However, development of culture-independent molecular techniques comprised of direct DNA extraction from faeces followed by sequencing, offer new opportunities to estimate the occurrence of eukaryotes in the human gut by providing data on the entire eukaryotic community, particularly not-yet-cultured or fastidious organisms. Further broad surveys of the eukaryotic communities in the gut based on high throughput tools such as next generation sequencing might lead to uncovering the real diversity of these ubiquitous organisms in the human intestinal tract and discovering the unrecognized roles of these eukaryotes in modulating the host immune system and inducing changes in host gut physiology and ecosystem.

Effects of pH and sugar concentration in Zygosaccharomyces rouxii growth and time for spoilage in concentrated grape juice at isothermal and non-isothermal conditions

The effect of pH (1.7-3.2) and sugar concentration (64-68 °Brix) on the growth of Zygosaccharomyces rouxii MC9 using response surface methodology was studied. Experiments were carried out in concentrated grape juice inoculated with Z. rouxii at isothermal conditions (23 °C) for 60 days. pH was the variable with the highest effect on growth parameters (potential maximum growth rate and lag phase duration), although the effect of sugar concentration were also significant. In a second experiment, the time for spoilage by this microorganism in concentrated grape juice was evaluated at isothermal (23 °C) and non-isothermal conditions, in an effort to reproduce standard storage and overseas shipping temperature conditions, respectively. Results show that pH was again the environmental factor with the highest impact on delaying the spoilage of the product. Thereby, a pH value below 2.0 was enough to increase the shelf life of the product for more than 60 days in both isothermal and non-isothermal conditions. The information obtained in the present work could be used by producers and buyers to predict the growth and time for spoilage of Z. rouxii in concentrated grape juice.

Development and application of a loop-mediated isothermal amplification assay for rapid identification of aflatoxigenic molds and their detection in food samples

Aflatoxins are the most thoroughly studied mycotoxins. They are produced by several members of the genus Aspergillus in section Flavi with Aspergillus flavus, Aspergillus parasiticus, and Aspergillus nomius being frequently isolated from contaminated food sources. In this work, we describe the development and evaluation of loop-mediated isothermal amplification (LAMP) assays for rapid detection of the three species in separate analyses. The acl1-gene of A. flavus and amy1-genes of A. nomius and A. parasiticus were used as target genes. The detection limits were 2.4, 7.6 and 20pg of pure DNA/reaction for A. flavus, A. nomius and A. parasiticus, respectively. For specificity testing, DNA extracted from mycelia of representative strains of 39 Aspergillus species, 23 Penicillium species, 75 Fusarium species and 37 other fungal species was used as a template for the specific LAMP primer sets developed for the three target species. The LAMP assay was combined with a DNA extraction method for the analysis of pure fungal cultures as well as artificially contaminated Brazil nuts, peanuts and green coffee beans. It is suggested that the developed LAMP assay is a promising tool in the prediction of a potential aflatoxin risk in food and food raw materials and may therefore be suitable for high throughput analysis in the food industry.

Zygosaccharomyces gambellarensis sp. nov., an ascosporogenous yeast isolated from an Italian ‘passito’ style wine

Yeast strains were isolated from Vin Santo of Gambellara, a sweet white wine with the specificity of Controlled Designation of Origin produced from off-vine overripened grapes in the Veneto region (Italy). Comparative sequence analysis of the 26S rRNA gene revealed that three representative strains (ZO03-5T, CA06-8 and ME06-9) constitute a taxon related to, but distinct from, Zygosaccharomyces machadoi. Similarity between the 26S rRNA gene domain D1/D2 sequence of the three isolates and Z. machadoi was 97.9 %; moreover, the morphological characteristics and the physiological behaviour also supported recognition of a novel taxon of osmophilic non-psychrophilic yeast showing a flower-like arrangement of budding cells that remain attached to each other. The name Zygosaccharomyces gambellarensis is proposed for the novel species, with ZO03-5T ( = CBS 12191T = MUCL 53393T) as the type strain.

A reverse transcriptase PCR technique for the detection and viability assessment of Kluyveromyces marxianus in yoghurt

A fast and sensitive reverse transcriptase PCR (RT-PCR) method was developed for the detection of viable Kluyveromyces marxianus in yoghurt. Yeast-specific primers were used with the RT-PCR to evaluate the suitability of 18S rRNA as a target for the detection of viable yeasts in pure culture and yoghurt. The RT-PCR assay was able to detect down to 10(2) CFU ml(-1) in yoghurt samples contaminated with viable yeast cells. Application of the RT-PCR method to commercial yoghurt samples demonstrated the utility of this technique for detection of low concentrations of viable yeast cells in naturally contaminated dairy products. The 18S rRNA molecule is an appropriate target for cell viability assessment because of its limited persistence after cell death and the resultant high level of sensitivity of the assay.

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.

An inter-laboratory evaluation of selective media for the detection and enumeration of yeasts from blue-veined cheese

Five countries representative of laboratories 1-5 evaluated 11 different selective media, designed to suppress mould and bacterial growth and support yeasts growth, for the recovery of yeast populations from blue veined cheeses. In addition, qualitative results were also incorporated. The yeast enumeration values were subjected to statistical analysis using analysis of variance (ANOVA) and the Tukey-Kramer multiple comparison test. With the exception of Laboratory 3, none of the other laboratories was successful in recovering yeasts on all the media. Six of the media proved inadequate for the enumeration of yeasts in the mould invested environment and were therefore omitted from statistical analysis. No significant differences in quantitative data obtained on Rose-Bengal Chloramphenicol Agar (RBCA), Dichloran Rose-Bengal Chloramphenicol Agar (DRBC), Dichloran 18% Glycerol Agar (DG18), and Malt extract agar supplemented with NaCl and oxytetracycline (MES) were detected by four of the collaborating laboratories whereas one laboratory found RBCA to be superior for yeast enumeration. DG18 and Malt Extract Agar with Biphenyl (MEB), however, were ranked superior based on qualitative results compared to the other media, attributed to distinctive individual yeast colonies and mould inhibition. RBCA, DRBC, DG18, and MES on the other hand, all proved to be adequate in supporting yeast colony development for quantitative analysis in samples obtained from blue veined cheeses.

Enumeration of yeasts in dairy products: a comparison of immunological and genetic techniques

Enzyme-linked immunosorbent assay (ELISA) and PCR techniques have been developed for the detection of spoilage yeast species in dairy products. Polyclonal antibodies against live yeast cells (AY) were raised in rabbits by inoculation of a mixture of 10 yeast species frequently associated with dairy products spoilage. AY antibodies were used for the development of two ELISA formats (indirect and double-antibody sandwich ELISA) for the detection of yeast species in milk and yogurt. A PCR assay was also developed for yeast detection in dairy products, using primers designed to amplify a conserved 250-base pair fragment of the 18S rRNA of the yeast species. The results obtained in this work show that ELISA techniques using polyclonal antibodies against viable yeast cells are of limited value for the detection and enumeration of spoilage yeast species in dairy products. On the contrary, PCR amplification of a conserved region of the 18S rRNA of the yeast species allows the homogeneous detection of all the yeast species tested and, combined with an overnight enrichment of samples, could be used for the detection of low levels of viable spoilage yeast species in dairy products.

Comparison of dichloran 18% glycerol (DG18) agar with general purpose mycological media for enumerating food spoilage yeasts

Dichloran 18% glycerol (DG18) agar was originally developed to enumerate xerophilic foodborne moulds. However, some laboratories are using DG18 agar as a general medium to enumerate foodborne moulds and yeasts. A collaborative study, with the participation of seven laboratories, was undertaken to compare DG18 agar with dichloran rose bengal chloramphenicol (DRBC) agar, tryptone glucose yeast extract chloramphenicol (TGYC) agar, and plate count agar supplemented with chloramphenicol (PCAC) for enumerating 14 species of common food spoilage yeasts. Comparison of the mean values of populations of all yeasts recovered on each medium revealed no significant differences among DRBC agar, PCAC, and TGYC agar, while each of these media supported the development of significantly (P < or = 0.05) higher numbers of colonies than DG18 agar. However, differences were only 0.08 to 0.10 log10 cfu/ml, making the practical significance questionable. The overall coefficient of variation (CV) for within laboratory repeatability was 1.71%, while the CV for reproducibility of counts obtained among laboratories was 6.96%. Compared to DRBC agar, TGYC agar, and PCAC, yeast colonies were smaller on DG18 agar. Growth of Brettanomyces anomalus, Cryptococcus albidus, and Rhodotorula mucilaginosa was particularly retarded or inhibited on DG18 agar. Based on the performance of media in supporting colony development and ease of counting colonies, the use of DG18 agar as a general enumeration medium for foodborne yeasts cannot be recommended.

A collaborative study on media for the enumeration of yeasts in foods

A collaborative study was made to evaluate the effectivity of a general purpose medium, tryptone glucose yeast extract (TGY) agar on the detection and enumeration of yeasts from food. Nine laboratories participated in the study and compared five media (four kinds of TGY with different concentrations of glucose, one of them without tryptone, and, for comparison, dichloran rose bengal chloramphenicol (DRBC) agar). Six food samples were investigated by each laboratory and 23 additional food samples were investigated individually by different laboratories. No difference was found in the performance of media with either the samples common to all laboratories or the various samples tested in different ones. A medium consisting of tryptone, glucose and yeast extract, at any concentration of glucose tested, appeared reliable for the detection and enumeration of yeasts from foods, and its performance did not differ from that of DRBC. Omission of tryptone as recommended by ISO provided an even simpler medium of equally good performance. TGY without chloramphenicol may result in higher total counts due to the development of bacteria. DRBC incubated in light results in lower counts compared to that incubated in the dark.

Effect of diluent type on viability of yeasts enumerated from foods or pure culture

The effects of seven diluent types on the viability of yeasts enumerated from foods and in pure culture were studied. The diluents were laboratory glass distilled water; saline water (0.85% NaCl), sodium phosphate buffer (0.1 M, pH 7.0), 0.1% peptone, 0.1% yeast extract, 0.1% peptone in 0.1 M sodium phosphate buffer, pH 7.0, and 0.1% malt extract. For all foods studied, dilution in 0.1% peptone gave the highest counts, with saline and phosphate buffer diluents giving lower counts than those obtained with distilled water. When seven species of yeast were enumerated in pure culture, highest counts were obtained using 0.1% peptone as the diluent and, with three exceptions, all species gave higher counts when diluted in diluents other than distilled water. When yeast suspensions were held in diluents for up to 2 h before plating, cell death occurred. The extent of death was highest in distilled water, saline and phosphate buffer diluents. Cell death also occurred in 0.1% peptone, yeast extract and malt extract, but to a lesser degree.

Enumeration of xerophilic yeasts in the presence of xerophilic moulds: a collaborative study

A collaborative study was undertaken to compare the performance of Dichloran 18% Glycerol agar (DG18) with three other media widely used in food mycology, for the enumeration of xerophilic yeasts in the presence of xerophilic moulds. Oxytetracycline Glucose Yeast extract agar, (OGY), Dichloran Rose Bengal Chloramphenicol agar (DRBC) and Malt extract Yeast extract 50% Glucose agar (MY50G) were evaluated. Three reference samples (A, B, C) were prepared using skimmed milk powder inoculated with mixed lyophilized cultures of selected xerophilic yeasts and moulds, at levels around 10(4) to 10(5) CFU/g. Yeast species used were Candida glucosophila, C. versatilis, Zygosaccharomyces bailii and Z. rouxii, together with Eurotium spp. and some other moulds. Collaborators were asked to examine each sample twice, by dilution plating on the four media. Colonies were counted after 3, 5 and 7 days incubation at 25 degrees C. Fourteen participants from seven laboratories in six countries collaborated in this study. The ability of collaborators to detect and count yeasts after 5 and 7 days on DG18, DRBC and OGY varied depending on the sample. Few participants were able to count yeasts even after 7 days on MY50G. The overall results demonstrated that DG18 incubated 5 days at 25 degrees C was superior to the other three media tested for the enumeration of xerophilic yeasts in the presence of xerophilic moulds.

Evaluation of diluents and media for enumerating Zygosaccharomyces rouxii in blueberry syrup

Combinations of diluents and enumeration media were evaluated for their efficacy in enumerating Zygosaccharomyces rouxii in blueberry syrup (aw 0.818, 0.870 and 0.921). Diluents consisted of deionized water containing 0.1% peptone, 20%, 30%, 40% or 50% glucose, 50% glucose plus 0.05% Tween 80, and 12%, 18%, 26% or 35% glycerol, all calculated on a w/w basis. Enumeration media were dichloran rose bengal chloramphenicol (DRBC) agar, tryptone glucose yeast extract (TGY) agar, dichloran 18% glycerol (DG18) agar, plate count agar containing 52% sucrose (PCA52S) and malt extract yeast extract 50% glucose (MY50G) agar. Two test strains of Z. rouxii grown in blueberry syrup for 7 or 14 days responded similarly to diluent/enumeration medium combinations. The use of 0.1% peptone diluent or DRBC agar in combination with other enumeration media or diluents was inferior for recovering Z. rouxii. As the aw of the blueberry syrup decreased, the sensitivity of Z. rouxii to diluent containing decreased concentrations of glucose increased. The use of glycerol as a solute in diluent did not result in a similar trend, indicating that the protective effect of glycerol against osmotic stress to Z. rouxii cells is greater than that of glucose at high aw and that cells adapted to low aw in blueberry syrup are more sensitive to high aw in diluents. The addition of 0.05% Tween 80 to 50% glucose diluent did not influence performance. Overall, diluents containing 50% glucose (aw 0.898), 18% glycerol (aw 0.956) or 26% glycerol (0.934), in combination with TGY agar (aw 0.982), resulted in the highest recovery of Z. rouxii from blueberry syrup at aw 0.818 to 0.921.