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SaccharomycesIDentifier, SID: strain-level analysis of Saccharomyces cerevisiae populations by using microsatellite meta-patterns. Sci Rep 2017; 7:15343. [PMID: 29127392 PMCID: PMC5681646 DOI: 10.1038/s41598-017-15729-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 10/24/2017] [Indexed: 01/09/2023] Open
Abstract
Saccharomyces cerevisiae is a common yeast with several applications, among which the most ancient is winemaking. Because individuals belonging to this species show a wide genetic and phenotypic variability, the possibility to identify the strains driving fermentation is pivotal when aiming at stable and palatable products. Metagenomic sequencing is increasingly used to decipher the fungal populations present in complex samples such as musts. However, it does not provide information at the strain level. Microsatellites are commonly used to describe the genotype of single strains. Here we developed a population-level microsatellite profiling approach, SID (Saccharomyces cerevisiae IDentifier), to identify the strains present in complex environmental samples. We optimized and assessed the performances of the analytical procedure on patterns generated in silico by computationally pooling Saccharomyces cerevisiae microsatellite profiles, and on samples obtained by pooling DNA of different strains, proving its ability to characterize real samples of grape wine fermentations. SID showed clear differences among S. cerevisiae populations in grape fermentation samples, identifying strains that are likely composing the populations and highlighting the impact of the inoculation of selected exogenous strains on natural strains. This tool can be successfully exploited to identify S. cerevisiae strains in any kind of complex samples.
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Mohammed YF, Salem EZ, Shahin IMI, Abdo HM, Emam HE, Fawzy M, Abdel Salam MF. Applicability of Fourier transform infrared (FTIR) spectroscopy in rapid identification of some Candida and dermatophyte species infections in humans. Int J Dermatol 2016; 55:1164-71. [PMID: 27337493 DOI: 10.1111/ijd.4957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2009] [Revised: 08/15/2010] [Accepted: 09/23/2010] [Indexed: 11/26/2022]
Abstract
Traditional systems of identifying yeasts and dermatophytes have many disadvantages. Preliminary data on a radically different approach based on optical spectroscopic techniques suggest that these techniques may offer some advantages. We conducted a trial to verify the practical applicability of Fourier transform infrared (FTIR) spectroscopy in the identification of some yeast and dermatophyte species, in which samples from 50 patients with superficial fungal infections were cultured on Sabouraud dextrose agar with chloramphenicol and cycloheximide (actidione) and studied using FTIR microspectroscopy. Spectra of the same species were identical, whereas spectra of different species did not show similarity. This study showed that FTIR microspectroscopy is promising and can be used to obtain, with a single measurement, a "molecular fingerprint" of Candida and dermatophyte species. It can be improved further in terms of reliability.
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Affiliation(s)
- Yaser F Mohammed
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt.
| | - Elsayed Z Salem
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Ibrahim M I Shahin
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Hamed M Abdo
- Department of Dermatology, Venereology and Andrology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Hanaa E Emam
- Department of Dermatology and Venereology, National Research Center, Cairo, Egypt
| | - Mahmoud Fawzy
- Department of Dermatology and Venereology, National Research Center, Cairo, Egypt
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Stefanini I, Albanese D, Cavazza A, Franciosi E, De Filippo C, Donati C, Cavalieri D. Dynamic changes in microbiota and mycobiota during spontaneous 'Vino Santo Trentino' fermentation. Microb Biotechnol 2016; 9:195-208. [PMID: 26780037 PMCID: PMC4767281 DOI: 10.1111/1751-7915.12337] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/19/2015] [Accepted: 10/28/2015] [Indexed: 02/03/2023] Open
Abstract
Vino Santo is a sweet wine produced from late harvesting and pressing of Nosiola grapes in a small, well-defined geographical area in the Italian Alps. We used metagenomics to characterize the dynamics of microbial communities in the products of three wineries, resulting from spontaneous fermentation with almost the same timing and procedure. Comparing fermentation dynamics and grape microbial composition, we show a rapid increase in a small number of wine yeast species, with a parallel decrease in complexity. Despite the application of similar protocols, slight changes in the procedures led to significant differences in the microbiota in the three cases of fermentation: (i) fungal content of the must varied significantly in the different wineries, (ii) Pichia membranifaciens persisted in only one of the wineries, (iii) one fermentation was characterized by the balanced presence of Saccharomyces cerevisiae and Hanseniaspora osmophila during the later phases. We suggest the existence of a highly winery-specific 'microbial-terroir' contributing significantly to the final product rather than a regional 'terroir'. Analysis of changes in abundance during fermentation showed evident correlations between different species, suggesting that fermentation is the result of a continuum of interaction between different species and physical-chemical parameters.
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Affiliation(s)
- Irene Stefanini
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Davide Albanese
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Agostino Cavazza
- Food Quality Nutrition & Health Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Elena Franciosi
- Food Quality Nutrition & Health Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Carlotta De Filippo
- Food Quality Nutrition & Health Department, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.,Institute of Biometeorology - IBIMET, National Research Council, Florence, Italy
| | - Claudio Donati
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy
| | - Duccio Cavalieri
- Department of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach (FEM), San Michele all'Adige, Italy.,Institute of Biometeorology - IBIMET, National Research Council, Florence, Italy.,Department of Biology, University of Florence, Florence, Italy
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Gallardo G, Ruiz-Moyano S, Hernández A, Benito MJ, Córdoba MG, Pérez-Nevado F, Martín A. Application of ISSR-PCR for rapid strain typing of Debaryomyces hansenii isolated from dry-cured Iberian ham. Food Microbiol 2014; 42:205-11. [PMID: 24929738 DOI: 10.1016/j.fm.2014.03.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/14/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
Yeast populations of dry-cured Iberian ham isolated from seven industries in the province of Badajoz were characterized by ISSR-PCR using the (CAG)4 primer and PCR-RFLP of the ITS1-5.8S rRNA-ITS2 fragment, and identified by DNA sequencing. A total of 242 isolates were analyzed, indicating the primary species present was Debaryomyces hansenii at 80.9% of the isolates followed by Candida zeylanoides at 10.3% of the isolates. The remainders of isolates were identified as Yamadazyma triangularis, Sporobolomyces roseus, Meyerozyma guilliermondii, Rhodotorula slooffiae, and Cryptococcus victoriae. The ISSR-PCR method was a fast and reliable method which was able to discriminate species at a level comparable to restriction analyses of the ITS1-5.8S rRNA-ITS2 region. This method allowed for strain typing of D. hansenii, yielding 29 different PCR patterns within 196 isolates. Moreover, ISSR-PCR using the (CAG)4 primer indicated that this technique could be a promising tool for rapid discrimination of yeast starter cultures and spoilage species in dry-cured Iberian ham.
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Affiliation(s)
- G Gallardo
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain
| | - S Ruiz-Moyano
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain
| | - A Hernández
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain.
| | - M J Benito
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain
| | - M G Córdoba
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain
| | - F Pérez-Nevado
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain
| | - A Martín
- Nutrición y Bromatología, Escuela de Ingenierías Agrarias, Universidad de Extremadura, Av. Adolfo Suarez, 06007 Badajoz, Spain
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Padilla B, Manzanares P, Belloch C. Yeast species and genetic heterogeneity within Debaryomyces hansenii along the ripening process of traditional ewes' and goats' cheeses. Food Microbiol 2014; 38:160-6. [DOI: 10.1016/j.fm.2013.09.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/27/2013] [Accepted: 09/08/2013] [Indexed: 11/29/2022]
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Fadda M, Pisano M, Scaccabarozzi L, Mossa V, Deplano M, Moroni P, Liciardi M, Cosentino S. Use of PCR-restriction fragment length polymorphism analysis for identification of yeast species isolated from bovine intramammary infection. J Dairy Sci 2013; 96:7692-7. [DOI: 10.3168/jds.2013-6996] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 08/16/2013] [Indexed: 11/19/2022]
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Barszczewski W, Robak M. PCR-Based Differentiation and Homology of Brewing and Type Strains of the Genus Saccharomyces. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2006.tb00246.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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9
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Senses-Ergul S, Karasu-Yalcin S, Ozbas ZY. Molecular identification of some yeast strains isolated from various sugary foods. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-011-0404-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Rahim MBH, Syed MA, Shukor MY. Isolation and characterization of an acrylamide-degrading yeast Rhodotorula sp. strain MBH23 KCTC 11960BP. J Basic Microbiol 2011; 52:573-81. [PMID: 22144174 DOI: 10.1002/jobm.201100116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Accepted: 08/27/2011] [Indexed: 11/06/2022]
Abstract
As well as for chemical and environmental reasons, acrylamide is widely used in many industrial applications. Due to its carcinogenicity and toxicity, its discharge into the environment causes adverse effects on humans and ecology alike. In this study, a novel acrylamide-degrading yeast has been isolated. The isolate was identified as Rhodotorula sp. strain MBH23 using ITS rRNA analysis. The results showed that the best carbon source for growth was glucose at 1.0% (w/v). The optimum acrylamide concentration, being a nitrogen source for cellular growth, was at 500 mg l(-1). The highest tolerable concentration of acrylamide was 1500 mg l(-1) whereas growth was completely inhibited at 2000 mg l(-1). At 500 mg l(-1), the strain MBH completely degraded acrylamide on day 5. Acrylic acid as a metabolite was detected in the media. Strain MBH23 grew well between pH 6.0 and 8.0 and between 27 and 30 °C. Amides such as 2-chloroacetamide, methacrylamide, nicotinamide, acrylamide, acetamide, and propionamide supported growth. Toxic heavy metals such as mercury, chromium, and cadmium inhibited growth on acrylamide.
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Affiliation(s)
- M B H Rahim
- Department of Biochemistry, University Putra Malaysia, UPM Serdang, Selangor, Malaysia
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Yalcin SK, Bozdemir MT, Ozbas ZY. Utilization of Whey and Grape Must for Citric Acid Production by TwoYarrowia lipolyticaStrains. FOOD BIOTECHNOL 2009. [DOI: 10.1080/08905430903106860] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Bockelmann W, Heller M, Heller KJ. Identification of yeasts of dairy origin by amplified ribosomal DNA restriction analysis (ARDRA). Int Dairy J 2008. [DOI: 10.1016/j.idairyj.2008.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Álvarez-Martín P, Flórez AB, López-Díaz TM, Mayo B. Phenotypic and molecular identification of yeast species associated with Spanish blue-veined Cabrales cheese. Int Dairy J 2007. [DOI: 10.1016/j.idairyj.2006.11.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Belén Flórez A, Álvarez-Martín P, López-Díaz TM, Mayo B. Morphotypic and molecular identification of filamentous fungi from Spanish blue-veined Cabrales cheese, and typing of Penicillium roqueforti and Geotrichum candidum isolates. Int Dairy J 2007. [DOI: 10.1016/j.idairyj.2006.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Senses-Ergul S, Agoston R, Belák A, Deák T. Characterization of some yeasts isolated from foods by traditional and molecular tests. Int J Food Microbiol 2006; 108:120-4. [PMID: 16388865 DOI: 10.1016/j.ijfoodmicro.2005.10.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2005] [Revised: 10/13/2005] [Accepted: 10/13/2005] [Indexed: 11/19/2022]
Abstract
In this study, 22 yeast strains isolated from foods were characterized by traditional and molecular techniques. With the help of traditional identification tests, yeast strains were grouped in 12 species belonging to 11 genera as follows: Candida parapsilosis, Rhodotorula mucilaginosa, Debaryomyces hansenii, Cryptococcus humicolus, Cryptococcus albidus, Aureobasidium spp., Hanseniaspora valbyensis, Metschnikowia pulcherrima, Lachancea thermotolerans, Pichia anomala, Geotrichum candidum and Yarrowia lipolytica. The patterns obtained by the digestion of ITS-18S rRNA gene with MspI and HaeIII restriction endonucleases were similar among strains belonging to the same species. With the help of randomly amplified polymorphic DNA (RAPD) analysis performed within the same species, discrimination of M. pulcherrima strains could be achieved.
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Affiliation(s)
- Sule Senses-Ergul
- Hacettepe University, Faculty of Engineering, Food Engineering Department, Beytepe 06532, Ankara, Turkey
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Beh AL, Fleet GH, Prakitchaiwattana C, Heard GM. Evaluation of molecular methods for the analysis of yeasts in foods and beverages. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2006; 571:69-106. [PMID: 16408594 DOI: 10.1007/0-387-28391-9_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Affiliation(s)
- Ai Lin Beh
- Food Science and Technology, School of Chemical Engineering and Industrial Chemistry, University of New South Wales, Sydney, Australia
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Péter G, Dlauchy D, Tornai-Lehoczki J, Kurtzman CP. Kuraishia MolischianaSp. Nov., the Teleomorph of Candida Molischiana. Antonie van Leeuwenhoek 2005; 88:241-7. [PMID: 16284930 DOI: 10.1007/s10482-005-7267-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Accepted: 05/12/2005] [Indexed: 11/27/2022]
Abstract
Thirty-two strains, many of them isolated from wood-associated habitats, and designated as Kuraishia (Pichia) capsulata and Candida molischiana according to their phenotype, exhibited two types of HaeIII restriction fragment patterns of their small subunit rDNA with the neighboring ITS. One fragment pattern corresponded to that of the type strain of K. capsulata, whereas the other pattern was unique to the typestrain of C. molischiana. Sequencing of the D1/D2 domain of the large subunit rDNA confirmed that the different HaeIII restriction fragment patterns of small subunit rDNA with the neighboring ITS reliably distinguished K. capsulata from C. molischiana. Ascospore formation was observed in several C. molischiana strains and K. molischiana (type strain: NCAIM Y.01725, CBS 9993) is proposed as the teleomorphic state of Candida molischiana.
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MESH Headings
- DNA Fingerprinting
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- DNA, Ribosomal Spacer/genetics
- DNA, Ribosomal Spacer/metabolism
- Deoxyribonucleases, Type II Site-Specific/metabolism
- Molecular Sequence Data
- Mycological Typing Techniques
- Phylogeny
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- Saccharomycetales/classification
- Saccharomycetales/cytology
- Saccharomycetales/isolation & purification
- Saccharomycetales/physiology
- Sequence Analysis, DNA
- Spores, Fungal/cytology
- Wood
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Affiliation(s)
- Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Sciences, Corvinus University of Budapest, Somlói út 14-16, H-1118 Budapest, Hungary.
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Kiskó G, Sharp R, Roller S. Chitosan inactivates spoilage yeasts but enhances survival of Escherichia coli O157:H7 in apple juice. J Appl Microbiol 2005; 98:872-80. [PMID: 15752333 DOI: 10.1111/j.1365-2672.2004.02527.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To develop new measures for controlling both spoilage and pathogenic micro-organisms in unpasteurized apple juice using chitosan. METHODS AND RESULTS Micro-organisms were isolated and identified from apple juice treated or untreated with chitosan using enrichment, selective media, microscopy, substrate assimilation patterns and ribosomal DNA profiling. Chitosan (0.05-0.1%) delayed spoilage by yeasts at 25 degrees C for up to 12 days but the effect was species specific: Kloeckera apiculata and Metschnikowia pulcherrima were inactivated but Saccharomyces cerevisiae and Pichia spp. multiplied slowly. In challenge experiments at 25 degrees C, total yeast counts were 3-5 log CFU ml(-1) lower in chitosan-treated juices than in the controls for 4 days but the survival of Escherichia coli O157:H7 was extended from 1 to 2 days; at 4 degrees C, chitosan reduced the yeast counts by 2-3 log CFU ml(-1) for up to 10 days but survival of the pathogen was prolonged from 3 to 5 days. The survival of Salmonella enterica serovar Typhimurium was unaffected by chitosan at either temperature. CONCLUSIONS The addition of chitosan to apple juice delayed spoilage by yeasts but enhanced the survival of E. coli O157:H7. SIGNIFICANCE AND IMPACT OF THE STUDY The results suggest that the use of chitosan in the treatment of fruit juices may potentially lead to an increased risk of food poisoning from E. coli O157:H7.
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Affiliation(s)
- G Kiskó
- Szent István University, Budapest, Hungary
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Péter G, Tornai-Lehoczki J, Suzuki M, Dlauchy D. Metschnikowia viticola sp. nov., a new yeast species from grape. Antonie van Leeuwenhoek 2005; 87:155-60. [PMID: 15723177 DOI: 10.1007/s10482-004-2842-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Accepted: 09/02/2004] [Indexed: 10/25/2022]
Abstract
Two yeast strains, producing needle-shaped ascospores under suitable conditions, were isolated from grapes grown in Hungary. Based on these two strains, Metschnikowia viticola (type strain NCAIM Y.01705, CBS 9950, JCM 12561) is proposed as a new yeast species. Considering its phenotypic features, the restriction fragment patterns of 18S rDNA and the sequence of the D1/D2 domain of 26S rDNA, the proposed new species is closely related to Candida kofuensis.
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MESH Headings
- Candida/classification
- Candida/genetics
- DNA Fingerprinting
- DNA, Fungal/chemistry
- DNA, Fungal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Genes, rRNA
- Hungary
- Molecular Sequence Data
- Mycological Typing Techniques
- Phylogeny
- Polymorphism, Restriction Fragment Length
- RNA, Fungal/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- Saccharomycetales/classification
- Saccharomycetales/cytology
- Saccharomycetales/isolation & purification
- Saccharomycetales/physiology
- Sequence Analysis, DNA
- Vitis/microbiology
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Affiliation(s)
- Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Budapest University of Economic Sciences and Public Administration, Somlói út 14-16, H-1118, Budapest, Hungary.
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Romero P, Patiño B, Quirós M, González-Jaén MT, Valderrama MJ, de Silóniz MI, Peinado JM. Differential detection of isolated from intermediate-moisture foods by PCR-RFLP of the IGS region of rDNA. FEMS Yeast Res 2005; 5:455-61. [PMID: 15691750 DOI: 10.1016/j.femsyr.2004.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2004] [Revised: 04/14/2004] [Accepted: 09/10/2004] [Indexed: 02/06/2023] Open
Abstract
The amplification by PCR of the Intergenic Spacer region (IGS) of rDNA followed by Restriction Fragment Length Polymorphism (RFLP) analysis was evaluated as a potential method for the identification of Debaryomyces hansenii among other yeast species that frequently contaminate Intermediate-Moisture Foods (IMFs). For a first rapid differentiation at the species level, the determination of the IGS-PCR fragment size was found to be a useful approach. The digestion of this region with the enzymes HhaI, HapII and MboI resulted in specific patterns that permit the identification of D. hansenii among other yeast species. This method also permitted the discrimination between the D. hansenii varieties (var. hansenii and var. fabryi) as well as the differentiation of D. hansenii from other species of the genus, such as Debaryomyces pseudopolymorphus or Debaryomyces polymorphus var. polymorphus. The IGS-PCR RFLP method was assayed for the differential detection of D. hansenii in contaminated or spoiled IMF products and compared with traditional identification procedures, resulting in a 100% detection rate for D. hansenii.
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Affiliation(s)
- Patricia Romero
- Departamento de Microbiología, Facultad de Biología, Universidad Complutense de Madrid, C/José Antonio Novais No. 2, 28040 Madrid, Spain
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Naumova ES, Gazdiev DO, Naumov GI. Molecular divergence of the soil yeasts Williopsis sensu stricto. Microbiology (Reading) 2004. [DOI: 10.1007/s11021-005-0007-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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22
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Morrissey WF, Davenport B, Querol A, Dobson ADW. The role of indigenous yeasts in traditional Irish cider fermentations. J Appl Microbiol 2004; 97:647-55. [PMID: 15281947 DOI: 10.1111/j.1365-2672.2004.02354.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIMS To study the role of the indigenous yeast flora in traditional Irish cider fermentations. METHODS AND RESULTS Wallerstein laboratory nutrient agar supplemented with biotin, ferric ammonium citrate, calcium carbonate and ethanol was employed together with PCR-restriction fragment length polymorphism analysis of the region spanning the internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene in the identification of indigenous yeasts at the species level, from traditional Irish cider fermentations. By combining the molecular approach and the presumptive media it was possible to distinguish between a large number of yeast species, and to track them within cider fermentations. The Irish cider fermentation process can be divided into three sequential phases based on the predominant yeast type present. Kloeckera/Hanseniaspora uvarum type yeasts predominate in the initial 'fruit yeast phase'. Thereafter Saccharomyces cerevisiae type yeast dominate in the 'fermentation phase', where the alcoholic fermentation takes place. Finally the 'maturation phase' which follows, is dominated by Dekkera and Brettanomyces type yeasts. H. uvarum type yeast were found to have originated from the fruit. Brettanomyces type yeast could be traced back to the press house, and also to the fruit. The press house was identified as having high levels of S. cerevisiae type yeast. A strong link was noted between the temperature profile of the cider fermentations, which ranged from 22 to 35 degrees C and the yeast strain population dynamics. CONCLUSIONS Many different indigenous yeast species were identified. The mycology of Irish cider fermentations appears to be very similar to that which has previously been reported in the wine industry. SIGNIFICANCE AND IMPACT OF THE STUDY This study has allowed us to gain a better understanding of the role of indigenous yeast species in 'Natural' Irish cider fermentations.
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Affiliation(s)
- W F Morrissey
- National Food Biotechnology Centre, University College Cork, National University of Ireland, Cork, Ireland
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Barszczewski W, Robak M. Differentiation of contaminating yeasts in brewery by PCR-based techniques. Food Microbiol 2004. [DOI: 10.1016/s0740-0020(03)00071-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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Deák R, Bodai L, Aarts HJM, Maráz A. Development of a novel, simple and rapid molecular identification system for clinicalCandidaspecies. Med Mycol 2004; 42:311-8. [PMID: 15473355 DOI: 10.1080/13693780310001624574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Identification of clinical yeast isolates causing candidiasis is routinely performed by commercial yeast identification systems based on biochemical, morphological and physiological tests. These systems require 3-5 days and the proportion of identifications that are incorrect is high. Our novel and rapid molecular identification system for clinical Candida species is based on the analysis of restriction patterns obtained from PCR-generated ribosomal DNA sequences using five restriction enzymes. A software package (CandID) was designed to include a database of restriction fragment length polymorphism (RFLP) patterns for 29 Candida species. For 'in-house' validation, 122 clinical isolates that had previously identified in clinical laboratories were typed by this system. These clinical isolates were also independently re-identified by the API 20C AUX system. The ribosomal DNA RFLP database in the context of supporting analytical software allowed simple and rapid (1 work day) identification.
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Affiliation(s)
- R Deák
- Department of Microbiology and Biotechnology Faculty of Food Science, Szent István University, Budapest.
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Casey GD, Dobson ADW. 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. J Appl Microbiol 2003; 95:13-22. [PMID: 12807449 DOI: 10.1046/j.1365-2672.2003.01940.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
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.
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Affiliation(s)
- G D Casey
- Department of Microbiology, and National Food Biotechnology Centre, University College, Cork, Ireland
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26
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Naumova ES, Korshunova IV, Jespersen L, Naumov GI. Molecular genetic identification of Saccharomyces sensu stricto strains from African sorghum beer. FEMS Yeast Res 2003; 3:177-84. [PMID: 12702450 DOI: 10.1016/s1567-1356(02)00191-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Genetic relationships of 24 phenotypically different strains isolated from sorghum beer in West Africa and the type cultures of the Saccharomyces sensu stricto species were investigated by universally primed polymerase chain reaction (PCR) analysis, microsatellite fingerprinting and PCR-restriction fragment length polymorphism (RFLP) of the ribosomal internal transcribed spacers. The results demonstrate that internal transcribed spacer (ITS) PCR-RFLP analysis with the endonucleases HaeIII, HpaII, ScrFI and TaqI is useful for discriminating S. cerevisiae, S. kudriavzevii, S. mikatae from one another and from the S. bayanus/S. pastorianus and S. cariocanus/S. paradoxus pairs. The sorghum beer strains exhibited the same restriction patterns as the type culture of S. cerevisiae CBS 1171. PCR profiles generated with the microsatellite primer (GTG)(5) and the universal primer N21 were almost identical for all isolates and strain CBS 1171. Despite phenotypic peculiarities, the strains involved in sorghum beer production in Ghana and Burkina Faso belong to S. cerevisiae. However, based on sequencing of the rDNA ITS1 region and Southern hybridisation analysis, these strains represent a divergent population of S. cerevisiae.
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MESH Headings
- Base Sequence
- Beer/microbiology
- Blotting, Southern
- Burkina Faso
- DNA Fingerprinting
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Electrophoresis, Gel, Pulsed-Field
- Genetic Variation
- Ghana
- Microsatellite Repeats/genetics
- Molecular Sequence Data
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- Saccharomyces/classification
- Saccharomyces/genetics
- Saccharomyces/metabolism
- Sequence Alignment
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Affiliation(s)
- Elena S Naumova
- State Institute for Genetics and Selection of Industrial Microorganisms, I-Dorozhnyi 1, Moscow 117545, Russia
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27
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Las Heras-Vazquez FJ, Mingorance-Cazorla L, Clemente-Jimenez JM, Rodriguez-Vico F. Identification of yeast species from orange fruit and juice by RFLP and sequence analysis of the 5.8S rRNA gene and the two internal transcribed spacers. FEMS Yeast Res 2003; 3:3-9. [PMID: 12702240 DOI: 10.1111/j.1567-1364.2003.tb00132.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Yeast isolates from orange fruit and juice in a spontaneous fermentation were identified and classified by two molecular techniques. The first was analysis of the restriction pattern generated from the polymerase chain reaction (PCR)-amplified 5.8S rRNA gene and the two internal transcribed spacers (ITS) using specific primers. The second technique was sequence analysis of the ITS regions using the same two primers. Nine different restriction profiles were obtained from the size of the PCR products and the restriction analyses with three endonucleases (CfoI, HaeIII and HinfI). These groups were identified as Candida tropicalis, Clavispora lusitaniae, Hanseniaspora uvarum, Pichia anomala, Pichia fermentans, Rhodotorula mucilaginosa, Saccharomyces cerevisiae, Saccharomyces unisporus, and Trichosporon asahii. Checking against identification according to morphological, physiological and biochemical traits corroborated this molecular identification. A total concordance was found in the identification with PCR-restriction fragment length polymorphism of the ITS region after analysing certified yeast strains from two different culture collections. Consequently, a rapid and reliable identification of the yeast populations was achieved by using molecular techniques.
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Affiliation(s)
- Francisco Javier Las Heras-Vazquez
- Departamento de Química-Física, Bioquímica y Química Inorgánica, Edificio C.I.T.E. I, Universidad de Almería, E-04120, La Cañada de San Urbano, Spain
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Wenning M, Seiler H, Scherer S. Fourier-transform infrared microspectroscopy, a novel and rapid tool for identification of yeasts. Appl Environ Microbiol 2002; 68:4717-21. [PMID: 12324312 PMCID: PMC126420 DOI: 10.1128/aem.68.10.4717-4721.2002] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2002] [Accepted: 07/02/2002] [Indexed: 11/20/2022] Open
Abstract
Fourier-transform infrared (FT-IR) microspectroscopy was used in this study to identify yeasts. Cells were grown to microcolonies of 70 to 250 micro m in diameter and transferred from the agar plate by replica stamping to an IR-transparent ZnSe carrier. IR spectra of the replicas on the carrier were recorded using an IR microscope coupled to an IR spectrometer, and identification was performed by comparison to reference spectra. The method was tested by using small model libraries comprising reference spectra of 45 strains from 9 genera and 13 species, recorded with both FT-IR microspectroscopy and FT-IR macrospectroscopy. The results show that identification by FT-IR microspectroscopy is equivalent to that achieved by FT-IR macrospectroscopy but the time-consuming isolation of the organisms prior to identification is not necessary. Therefore, this method also provides a rapid tool to analyze mixed populations. Furthermore, identification of 21 Debaryomyces hansenii and 9 Saccharomyces cerevisiae strains resulted in 92% correct identification at the strain level for S. cerevisiae and 91% for D. hansenii, which demonstrates that the resolution power of FT-IR microspectroscopy may also be used for yeast typing at the strain level.
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Affiliation(s)
- Mareike Wenning
- Microbial Ecology Group, Department of Biosciences, Technische Universität München, D-85350 Freising, Germany
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Deák T. Application of molecular techniques in wine microbiology. ACTA ALIMENTARIA 2002. [DOI: 10.1556/aalim.31.2002.1.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Cadez N, Raspor P, de Cock AWAM, Boekhout T, Smith MT. Molecular identification and genetic diversity within species of the genera Hanseniaspora and Kloeckera. FEMS Yeast Res 2002; 1:279-89. [PMID: 12702331 DOI: 10.1111/j.1567-1364.2002.tb00046.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Three molecular methods, RAPD-PCR analysis, electrophoretic karyotyping and RFLP of the PCR-amplified ITS regions (ITS1, ITS2 and the intervening 5.8S rDNA), were studied for accurate identification of Hanseniaspora and Kloeckera species as well as for determining inter- and intraspecific relationships of 74 strains isolated from different sources and/or geographically distinct regions. Of these three methods, PCR-RFLP analysis of ITS regions with restriction enzymes DdeI and HinfI is proposed as a rapid identification method to discriminate unambiguously between all six Hanseniaspora species and the single non-ascospore-forming apiculate yeast species Kloeckera lindneri. Electrophoretic karyotyping produced chromosomal profiles by which the seven species could be divided into four groups sharing similar karyotypes. Although most of the 60 strains examined exhibited a common species-specific pattern, a different degree of chromosomal-length polymorphism and a variable number of chromosomal DNA fragments were observed within species. Cluster analysis of the combined RAPD-PCR fingerprints obtained with one 10-mer primer, two microsatellite primers and one minisatellite primer generated clusters which with a few exceptions are in agreement with the groups as earlier recognized in DNA-DNA homology studies.
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Affiliation(s)
- Neza Cadez
- Biotechnical Faculty, Department of Food Science and Technology, University of Ljubljana, Slovenia
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