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The role of Nucleic Acid Mimics (NAMs) on FISH-based techniques and applications for microbial detection. Microbiol Res 2022; 262:127086. [PMID: 35700584 DOI: 10.1016/j.micres.2022.127086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 01/07/2023]
Abstract
Fluorescent in situ hybridization (FISH) is a powerful tool that for more than 30 years has allowed to detect and quantify microorganisms as well as to study their spatial distribution in three-dimensional structured environments such as biofilms. Throughout these years, FISH has been improved in order to face some of its earlier limitations and to adapt to new research objectives. One of these improvements is related to the emergence of Nucleic Acid Mimics (NAMs), which are now employed as alternatives to the DNA and RNA probes that have been classically used in FISH. NAMs such as peptide and locked nucleic acids (PNA and LNA) have provided enhanced sensitivity and specificity to the FISH technique, as well as higher flexibility in terms of applications. In this review, we aim to cover the state-of-the-art of the different NAMs and explore their possible applications in FISH, providing a general overview of the technique advancement in the last decades.
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2
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Zand E, Froehling A, Schoenher C, Zunabovic-Pichler M, Schlueter O, Jaeger H. Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review. Foods 2021; 10:3112. [PMID: 34945663 PMCID: PMC8701031 DOI: 10.3390/foods10123112] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022] Open
Abstract
As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.
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Affiliation(s)
- Elena Zand
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
| | - Antje Froehling
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Christoph Schoenher
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Marija Zunabovic-Pichler
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Oliver Schlueter
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Henry Jaeger
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
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3
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Branco P, Candeias A, Caldeira AT, González-Pérez M. A simple procedure for detecting Dekkera bruxellensis in wine environment by RNA-FISH using a novel probe. Int J Food Microbiol 2020; 314:108415. [PMID: 31707175 DOI: 10.1016/j.ijfoodmicro.2019.108415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 09/30/2019] [Accepted: 10/28/2019] [Indexed: 11/30/2022]
Abstract
Dekkera bruxellensis, considered the major microbial contaminant in wine production, produces 4-ethylphenol, a cause of unpleasant odors. Thus, identification of this yeast before wine spoilage is crucial. Although challenging, it could be achieved using a simple technique: RNA-FISH. To reach it is necessary to design probes that allow specific detection/identification of D. bruxellensis among the wine microorganisms and in the wine environment and, if possible, using low formamide concentrations. Therefore, this study was focused on: a) designing a DNA-FISH probe to identify D. bruxellensis that matches these requirements and b) determining the applicability of the RNA-FISH procedure after the end of the alcoholic fermentation and in wine. A novel DNA-FISH D. bruxellensis probe with good performance and specificity was designed. The application of this probe using an in-suspension RNA-FISH protocol (applying only 5% of formamide) allowed the early detection/identification of D. bruxellensis at low cell densities (5 × 102 cell/mL). This was possible by flow cytometry independently of the growth stage of the target cells, both at the end of the alcoholic fermentation and in wine even in the presence of high S. cerevisiae cell densities. Thus, this study aims to contribute to facilitate the identification of D. bruxellensis before wine spoilage occurs, preventing economic losses to the wine industry.
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Affiliation(s)
- Patrícia Branco
- HERCULES Laboratory, Évora University, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal
| | - António Candeias
- HERCULES Laboratory, Évora University, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; Chemistry Department, School of Sciences and Technology, Évora University, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - Ana Teresa Caldeira
- HERCULES Laboratory, Évora University, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; Chemistry Department, School of Sciences and Technology, Évora University, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - Marina González-Pérez
- HERCULES Laboratory, Évora University, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal.
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4
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Branco P, Candeias A, Caldeira AT, González‐Pérez M. An important step forward for the future development of an easy and fast procedure for identifying the most dangerous wine spoilage yeast, Dekkera bruxellensis, in wine environment. Microb Biotechnol 2019; 12:1237-1248. [PMID: 31197952 PMCID: PMC6801150 DOI: 10.1111/1751-7915.13422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 04/04/2019] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
Dekkera bruxellensis is the main reason for spoilage in the wine industry. It renders the products unacceptable leading to large economic losses. Fluorescence In Situ Hybridization (FISH) technique has the potential for allowing its specific detection. Nevertheless, some experimental difficulties can be encountered when FISH technique is applied in the wine environment (e.g. matrix and cells' autofluorescence, fluorophore inadequate selection and probes' low specificity to the target organisms). An easy and fast in-suspension RNA-FISH procedure was applied for the first time for identifying D. bruxellensis in wine. A previously designed RNA-FISH probe to detect D. bruxellensis (26S D. brux.5.1) was used, and the matrix and cells' fluorescence interferences, the influence of three fluorophores in FISH performance and the probe specificity were evaluated. The results revealed that to apply RNA-FISH technique in the wine environment, a red-emitting fluorophore should be used. Good probe performance and specificity were achieved with 25% of formamide. The resulting RNA-FISH protocol was applied in wine samples artificially inoculated with D. bruxellensis. This spoilage microorganism was detected in wine at cell densities lower than those associated with phenolic off-flavours. Thus, the RNA-FISH procedure described in this work represents an advancement to facilitate early detection of the most dangerous wine spoilage yeast and, consequently, to reduce the economic losses caused by this yeast to the wine industry.
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Affiliation(s)
- Patrícia Branco
- HERCULES LaboratoryÉvora UniversityLargo Marquês de Marialva 87000‐809ÉvoraPortugal
| | - António Candeias
- HERCULES LaboratoryÉvora UniversityLargo Marquês de Marialva 87000‐809ÉvoraPortugal
- Chemistry DepartmentSchool of Sciences and TechnologyÉvora UniversityRua Romão Ramalho 597000‐671ÉvoraPortugal
| | - Ana Teresa Caldeira
- HERCULES LaboratoryÉvora UniversityLargo Marquês de Marialva 87000‐809ÉvoraPortugal
- Chemistry DepartmentSchool of Sciences and TechnologyÉvora UniversityRua Romão Ramalho 597000‐671ÉvoraPortugal
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5
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Tubia I, Prasad K, Pérez-Lorenzo E, Abadín C, Zumárraga M, Oyanguren I, Barbero F, Paredes J, Arana S. Beverage spoilage yeast detection methods and control technologies: A review of Brettanomyces. Int J Food Microbiol 2018; 283:65-76. [DOI: 10.1016/j.ijfoodmicro.2018.06.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/21/2018] [Accepted: 06/25/2018] [Indexed: 12/28/2022]
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6
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Agnolucci M, Tirelli A, Cocolin L, Toffanin A. Brettanomyces bruxellensis yeasts: impact on wine and winemaking. World J Microbiol Biotechnol 2017; 33:180. [PMID: 28936776 DOI: 10.1007/s11274-017-2345-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/16/2017] [Indexed: 01/26/2023]
Abstract
Yeasts belonging to the Brettanomyces/Dekkera genus are non-conventional yeasts, which affect winemaking by causing wine spoilage all over the world. This mini-review focuses on recent results concerning the presence of Brettanomyces bruxellensis throughout the wine processing chain. Here, culture-dependent and independent methods to detect this yeast on grapes and at the very early stage of wine production are encompassed. Chemical, physical and biological tools, devised for the prevention and control of such a detrimental species during winemaking are also presented. Finally, the mini-review identifies future research areas relevant to the improvement of wine safety and sensory profiles.
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Affiliation(s)
- Monica Agnolucci
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124, Pisa, Italy.
| | - Antonio Tirelli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milano, Via Celoria 2, Milano, Italy
| | - Luca Cocolin
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - Annita Toffanin
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80, 56124, Pisa, Italy
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7
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Santos RS, Lima CC, Carvalho D, Meireles F, Guimarães N, Azevedo NF. Response surface methodology to optimize peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) in Saccharomyces cerevisiae. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.01.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Kuo HP, Wang R, Huang CY, Lai JT, Lo YC, Huang ST. Characterization of an extracellular β-glucosidase from Dekkera bruxellensis for resveratrol production. J Food Drug Anal 2017; 26:163-171. [PMID: 29389552 PMCID: PMC9332651 DOI: 10.1016/j.jfda.2016.12.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 12/05/2016] [Accepted: 12/25/2016] [Indexed: 12/11/2022] Open
Abstract
Polygonum cuspidatum is a widely grown crop with a rich source of polydatin (also called piceid) for resveratrol production. Resveratrol is produced from piceid via enzymatic cleavage of the sugar moiety of piceid. In this study, Dekkera bruxellensis mutants were selected based on their high p-nitrophenyl-β-d-glucopyranoside and piceid conversion activities. The enzyme responsible for piceid conversion was a heterodimeric protein complex that was predominantly secreted to the extracellular medium and consisted of two subunits at an equal ratio with molecular masses of 30.5 kDa and 48.3 kDa. The two subunits were identified as SCW4p and glucan-β-glucosidase precursor in D. bruxellensis. Both proteins were individually expressed in Saccharomyces cerevisiae exg1Δ mutants, which lack extracellular β-glucosidase activity, to confirm each protein’s enzymatic activities. Only the glucan-β-glucosidase precursor was shown to be a secretory protein with piceid deglycosylation activity. Our pilot experiments of piceid bioconversion demonstrate the possible industrial applications for this glucan-β-glucosidase precursor in the future.
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Affiliation(s)
- Hsiao-Ping Kuo
- Bioresources Collection and Research Center, Food Industry Research and Development Institute, Number 331, Shih-Pin Road, Hsinchu 30062, Taiwan
| | - Reuben Wang
- Institute of Food Science and Technology, National Taiwan University, Number 1, Section 4 Roosevelt Road, Taipei 10617, Taiwan
| | - Chiao-Ying Huang
- Bioresources Collection and Research Center, Food Industry Research and Development Institute, Number 331, Shih-Pin Road, Hsinchu 30062, Taiwan
| | - Jinn-Tsyy Lai
- Bioresources Collection and Research Center, Food Industry Research and Development Institute, Number 331, Shih-Pin Road, Hsinchu 30062, Taiwan
| | - Yi-Chen Lo
- Institute of Food Science and Technology, National Taiwan University, Number 1, Section 4 Roosevelt Road, Taipei 10617, Taiwan.
| | - Shyue-Tsong Huang
- Bioresources Collection and Research Center, Food Industry Research and Development Institute, Number 331, Shih-Pin Road, Hsinchu 30062, Taiwan.
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9
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A new method for the detection of early contamination of red wine by Brettanomyces bruxellensis using Pseudomonas putida 4-ethylphenol methylene hydroxylase (4-EPMH). Eur Food Res Technol 2016. [DOI: 10.1007/s00217-016-2822-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Longin C, Petitgonnet C, Guilloux-Benatier M, Rousseaux S, Alexandre H. Application of flow cytometry to wine microorganisms. Food Microbiol 2016; 62:221-231. [PMID: 27889152 DOI: 10.1016/j.fm.2016.10.023] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 07/20/2016] [Accepted: 10/11/2016] [Indexed: 02/07/2023]
Abstract
Flow cytometry (FCM) is a powerful technique allowing detection and enumeration of microbial populations in food and during food process. Thanks to the fluorescent dyes used and specific probes, FCM provides information about cell physiological state and allows enumeration of a microorganism in a mixed culture. Thus, this technique is increasingly used to quantify pathogen, spoilage microorganisms and microorganisms of interest. Since one decade, FCM applications to the wine field increase greatly to determine population and physiological state of microorganisms performing alcoholic and malolactic fermentations. Wine spoilage microorganisms were also studied. In this review we briefly describe FCM principles. Next, a deep revision concerning enumeration of wine microorganisms by FCM is presented including the fluorescent dyes used and techniques allowing a yeast and bacteria species specific enumeration. Then, the last chapter is dedicated to fluorescent dyes which are used to date in fluorescent microscopy but applicable in FCM. This chapter also describes other interesting "future" techniques which could be applied to study the wine microorganisms. Thus, this review seeks to highlight the main advantages of the flow cytometry applied to wine microbiology.
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Affiliation(s)
- Cédric Longin
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, F-21000 Dijon, France; Institut Universitaire de la Vigne et du Vin, Equipe VAlMiS, rue Claude Ladrey, BP 27877, F-21078 Dijon, France
| | - Clément Petitgonnet
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, F-21000 Dijon, France; Institut Universitaire de la Vigne et du Vin, Equipe VAlMiS, rue Claude Ladrey, BP 27877, F-21078 Dijon, France
| | - Michèle Guilloux-Benatier
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, F-21000 Dijon, France; Institut Universitaire de la Vigne et du Vin, Equipe VAlMiS, rue Claude Ladrey, BP 27877, F-21078 Dijon, France
| | - Sandrine Rousseaux
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, F-21000 Dijon, France; Institut Universitaire de la Vigne et du Vin, Equipe VAlMiS, rue Claude Ladrey, BP 27877, F-21078 Dijon, France
| | - Hervé Alexandre
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, F-21000 Dijon, France; Institut Universitaire de la Vigne et du Vin, Equipe VAlMiS, rue Claude Ladrey, BP 27877, F-21078 Dijon, France
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11
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Smith BD, Divol B. Brettanomyces bruxellensis, a survivalist prepared for the wine apocalypse and other beverages. Food Microbiol 2016; 59:161-75. [PMID: 27375257 DOI: 10.1016/j.fm.2016.06.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 06/07/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
Abstract
Brettanomyces bruxellensis is a common red wine spoilage yeast. Yet, in addition to wine, it has been isolated from other ecological niches that are just as nutritionally deficient as wine. B. bruxellensis can therefore be regarded as a survivor, well adapted to colonise harsh environments not often inhabited by other yeasts. This review is focused on the nutritional requirements of B. bruxellensis and the relevance thereof for its adaptation to the different matrices within which it occurs. Furthermore, the environmental conditions necessary (e.g. aerobic or anaerobic conditions) for the assimilation of the carbon or nitrogenous sources are discussed in this review. From literature, several confusing inconsistencies, regarding nutritional sources necessary for B. bruxellensis survival, in these specialist ecological niches are evidenced. The main focus of this review is wine but other products and niches that B. bruxellensis inhabits namely beer, cider, fruit juices and bioethanol production plants are also considered. This review highlights the lack of knowledge regarding B. bruxellensis when considering its nutritional requirements in comparison to Saccharomyces cerevisiae. However, there is a large enough body of evidence showing that the nutritional needs of B. bruxellensis are meagre, explaining its ability to colonise harsh environments.
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Affiliation(s)
- Brendan D Smith
- Institute of Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Benoit Divol
- Institute of Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
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12
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Identification of food and beverage spoilage yeasts from DNA sequence analyses. Int J Food Microbiol 2015; 213:71-8. [DOI: 10.1016/j.ijfoodmicro.2015.05.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 05/18/2015] [Accepted: 05/29/2015] [Indexed: 10/23/2022]
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13
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Kurtzman CP, Mateo RQ, Kolecka A, Theelen B, Robert V, Boekhout T. Advances in yeast systematics and phylogeny and their use as predictors of biotechnologically important metabolic pathways. FEMS Yeast Res 2015; 15:fov050. [PMID: 26136514 DOI: 10.1093/femsyr/fov050] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2015] [Indexed: 01/02/2023] Open
Abstract
Detection, identification and classification of yeasts have undergone a major transformation in the last decade and a half following application of gene sequence analyses and genome comparisons. Development of a database (barcode) of easily determined DNA sequences from domains 1 and 2 (D1/D2) of the nuclear large subunit rRNA gene and from ITS now permits many laboratories to identify species quickly and accurately, thus replacing the laborious and often inaccurate phenotypic tests previously used. Phylogenetic analysis of gene sequences is leading to a major revision of yeast systematics that will result in redefinition of nearly all genera. This new understanding of species relationships has prompted a change of rules for naming and classifying yeasts and other fungi, and these new rules are presented in the recently implemented International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). The use of molecular methods for species identification and the impact of Code changes on classification will be discussed, as will use of phylogeny for prediction of biotechnological applications.
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Affiliation(s)
- Cletus P Kurtzman
- Bacterial Foodborne Pathogens and Mycology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA
| | - Raquel Quintilla Mateo
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, B-3001 Leuven, Belgium Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Anna Kolecka
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
| | - Bart Theelen
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
| | - Vincent Robert
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
| | - Teun Boekhout
- CBS Fungal Biodiversity Centre (CBS-KNAW), 3584 CT Utrecht, the Netherlands
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Steensels J, Daenen L, Malcorps P, Derdelinckx G, Verachtert H, Verstrepen KJ. Brettanomyces yeasts--From spoilage organisms to valuable contributors to industrial fermentations. Int J Food Microbiol 2015; 206:24-38. [PMID: 25916511 DOI: 10.1016/j.ijfoodmicro.2015.04.005] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/23/2015] [Accepted: 04/03/2015] [Indexed: 12/13/2022]
Abstract
Ever since the introduction of controlled fermentation processes, alcoholic fermentations and Saccharomyces cerevisiae starter cultures proved to be a match made in heaven. The ability of S. cerevisiae to produce and withstand high ethanol concentrations, its pleasant flavour profile and the absence of health-threatening toxin production are only a few of the features that make it the ideal alcoholic fermentation organism. However, in certain conditions or for certain specific fermentation processes, the physiological boundaries of this species limit its applicability. Therefore, there is currently a strong interest in non-Saccharomyces (or non-conventional) yeasts with peculiar features able to replace or accompany S. cerevisiae in specific industrial fermentations. Brettanomyces (teleomorph: Dekkera), with Brettanomyces bruxellensis as the most commonly encountered representative, is such a yeast. Whilst currently mainly considered a spoilage organism responsible for off-flavour production in wine, cider or dairy products, an increasing number of authors report that in some cases, these yeasts can add beneficial (or at least interesting) aromas that increase the flavour complexity of fermented beverages, such as specialty beers. Moreover, its intriguing physiology, with its exceptional stress tolerance and peculiar carbon- and nitrogen metabolism, holds great potential for the production of bioethanol in continuous fermentors. This review summarizes the most notable metabolic features of Brettanomyces, briefly highlights recent insights in its genetic and genomic characteristics and discusses its applications in industrial fermentation processes, such as the production of beer, wine and bioethanol.
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Affiliation(s)
- Jan Steensels
- Laboratory for Genetics and Genomics, Department of Microbial and Molecular Systems (M(2)S), Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Luk Daenen
- AB-InBev SA/NV, Brouwerijplein 1, B-3000 Leuven, Belgium
| | | | - Guy Derdelinckx
- Centre for Food and Microbial Technology, Department of Microbial and Molecular Systems (M(2)S), LFoRCe, KU Leuven, Kasteelpark Arenberg 33, 3001 Leuven, Belgium
| | - Hubert Verachtert
- Centre for Food and Microbial Technology, Department of Microbial and Molecular Systems (M(2)S), LFoRCe, KU Leuven, Kasteelpark Arenberg 33, 3001 Leuven, Belgium
| | - Kevin J Verstrepen
- Laboratory for Genetics and Genomics, Department of Microbial and Molecular Systems (M(2)S), Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 22, 3001 Leuven, Belgium; Laboratory for Systems Biology, VIB, Bio-Incubator, Gaston Geenslaan 1, 3001 Leuven, Belgium.
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15
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Wang C, Esteve-Zarzoso B, Mas A. Monitoring of Saccharomyces cerevisiae, Hanseniaspora uvarum, and Starmerella bacillaris (synonym Candida zemplinina) populations during alcoholic fermentation by fluorescence in situ hybridization. Int J Food Microbiol 2014; 191:1-9. [PMID: 25218463 DOI: 10.1016/j.ijfoodmicro.2014.08.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/31/2014] [Accepted: 08/09/2014] [Indexed: 10/24/2022]
Abstract
Various molecular approaches have been applied as culture-independent techniques to monitor wine fermentations over the last decade. Among them, those based on RNA detection have been widely used for yeast cell detection, assuming that RNA only exists in live cells. Fluorescence in situ hybridization (FISH) targeting intracellular rRNA is considered a promising technique for the investigation of wine ecology. For the present study, we applied the FISH technique in combination with epifluorescence microscopy and flow cytometry to directly quantify populations of Saccharomyces cerevisiae, Hanseniaspora uvarum, and Starmerella bacillaris during alcoholic fermentations. A new specific probe that hybridizes with eight species of Hanseniaspora genus and a second probe specific for Starm. bacillaris were designed, and the conditions for their application to pure cultures, mixed cultures, and wine samples were optimized. Single and mixed fermentations were performed with natural, concentrated must at two different temperatures, 15 °C and 25 °C. The population dynamics revealed that the Sacch. cerevisiae population increased to 10(7)-10(8)cells/ml during all fermentations, whereas H. uvarum and Starm. bacillaris tended to increase in single fermentations but remained at levels similar to their inoculations at 10(6)cells/ml in mixed fermentations. Temperature mainly affected the fermentation duration (slower at the lower temperature) but did not affect the population sizes of the different species. The use of these probes in natural wine fermentations has been validated.
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Affiliation(s)
- Chunxiao Wang
- Departament de Bioquímica i Biotecnologia, Facultat d' Enologia, Universitat Rovira i Virgili, Marcel·lí Domingo s/n, Tarragona 43007, Spain
| | - Braulio Esteve-Zarzoso
- Departament de Bioquímica i Biotecnologia, Facultat d' Enologia, Universitat Rovira i Virgili, Marcel·lí Domingo s/n, Tarragona 43007, Spain.
| | - Albert Mas
- Departament de Bioquímica i Biotecnologia, Facultat d' Enologia, Universitat Rovira i Virgili, Marcel·lí Domingo s/n, Tarragona 43007, Spain
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PNA fluorescent in situ hybridization (FISH) for rapid microbiology and cytogenetic analysis. Methods Mol Biol 2014; 1050:167-78. [PMID: 24297359 DOI: 10.1007/978-1-62703-553-8_14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Hybridization-based assays for the detection of nucleic acids including in situ hybridization are increasingly being utilized in a wide variety of disciplines such as cytogenetics, microbiology, and histology. Generally in situ hybridization assays utilize either cloned genomic probes for the detection of DNA sequences or oligonucleotide probes for the detection of DNA or RNA sequences. Alternately, PNA probes are increasingly being utilized in a variety of in situ hybridization assays. The neutral backbone of the PNA molecule allows for the PNA probes to bind to DNA or RNA under low ionic strength conditions that will either disfavor reannealing of complimentary genomic sequences or are denaturing for RNA secondary structure but are favorable for PNA/DNA or PNA/RNA hybridization. For in situ hybridization assays these unique properties of PNA probes offer significant advantages that allow for the development of fast, simple, and robust assays (Figs. 14.1 and 14.2).
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Schifferdecker AJ, Dashko S, Ishchuk OP, Piškur J. The wine and beer yeast Dekkera bruxellensis. Yeast 2014; 31:323-32. [PMID: 24932634 PMCID: PMC4257070 DOI: 10.1002/yea.3023] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/19/2014] [Accepted: 06/02/2014] [Indexed: 11/26/2022] Open
Abstract
Recently, the non-conventional yeast Dekkera bruxellensis has been gaining more and more attention in the food industry and academic research. This yeast species is a distant relative of Saccharomyces cerevisiae and is especially known for two important characteristics: on the one hand, it is considered to be one of the main spoilage organisms in the wine and bioethanol industry; on the other hand, it is 'indispensable' as a contributor to the flavour profile of Belgium lambic and gueuze beers. Additionally, it adds to the characteristic aromatic properties of some red wines. Recently this yeast has also become a model for the study of yeast evolution. In this review we focus on the recently developed molecular and genetic tools, such as complete genome sequencing and transformation, to study and manipulate this yeast. We also focus on the areas that are particularly well explored in this yeast, such as the synthesis of off-flavours, yeast detection methods, carbon metabolism and evolutionary history. © 2014 The Authors. Yeast published by John Wiley & Sons, Ltd.
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Candida identification: a journey from conventional to molecular methods in medical mycology. World J Microbiol Biotechnol 2014; 30:1437-51. [PMID: 24379160 DOI: 10.1007/s11274-013-1574-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 12/02/2013] [Indexed: 12/17/2022]
Abstract
The incidence of Candida infections have increased substantially in recent years due to aggressive use of immunosuppressants among patients. Use of broad-spectrum antibiotics and intravascular catheters in the intensive care unit have also attributed with high risks of candidiasis among immunocompromised patients. Among Candida species, C. albicans accounts for the majority of superficial and systemic infections, usually associated with high morbidity and mortality often caused due to increase in antimicrobial resistance and restricted number of antifungal drugs. Therefore, early detection of candidemia and correct identification of Candida species are indispensable pre-requisites for appropriate therapeutic intervention. Since blood culture based methods lack sensitivity, and species-specific identification by conventional method is time-consuming and often leads to misdiagnosis within closely related species, hence, molecular methods may provide alternative for accurate and rapid identification of Candida species. Although, several molecular approaches have been developed for accurate identification of Candida species but the internal transcribed spacer 1 and 2 (ITS1 and ITS2) regions of the rRNA gene are being used extensively in a variety of formats. Of note, ITS sequencing and PCR-RFLP analysis of ITS region seems to be promising as a rapid, easy, and cost-effective method for identification of Candida species. Here, we review a number of existing techniques ranging from conventional to molecular approaches currently in use for the identification of Candida species. Further, advantages and limitations of these methods are also discussed with respect to their discriminatory power, reproducibility, and ease of performance.
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Čuš F, Bach B, Barnavon L, Pongrac VŽ. Analytical determination of Dolenjska region wines quality. Food Control 2013. [DOI: 10.1016/j.foodcont.2013.03.017] [Citation(s) in RCA: 10] [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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Identification and characterization of non-saccharomyces spoilage yeasts isolated from Brazilian wines. World J Microbiol Biotechnol 2013; 29:1019-27. [DOI: 10.1007/s11274-013-1265-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 01/14/2013] [Indexed: 10/27/2022]
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Inácio J, da Luz Martins M. Microscopic detection of yeasts using fluorescence in situ hybridization. Methods Mol Biol 2013; 968:71-82. [PMID: 23296886 DOI: 10.1007/978-1-62703-257-5_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Fluorescence in situ hybridization (FISH) has been widely used for the detection and identification of microorganisms in their natural environments. In this chapter we describe the use of a simple FISH-based protocol to detect and identify clinically relevant yeast species in culture and biological samples using Cryptococcus neoformans as a model. After fixation of cells with paraformaldehyde, the same are embedded in hybridization buffer containing specific fluorochrome-labeled oligonucleotide probes. After incubation and a subsequent washing step for removing unbound probes, samples are analyzed by epifluorescence microscopy.
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Affiliation(s)
- João Inácio
- Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa (IHMT/UNL), Lisboa, Portugal
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23
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Barbin P, Cheval JL, Gilis JF, Strehaiano P, Taillandier P. Diversity in Spoilage Yeast Dekkera/Brettanomyces bruxellensis Isolated from French Red Wine. Assessment During Fermentation of Synthetic Wine Medium. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2008.tb00307.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Andorra I, Monteiro M, Esteve-Zarzoso B, Albergaria H, Mas A. Analysis and direct quantification of Saccharomyces cerevisiae and Hanseniaspora guilliermondii populations during alcoholic fermentation by fluorescence in situ hybridization, flow cytometry and quantitative PCR. Food Microbiol 2011; 28:1483-91. [DOI: 10.1016/j.fm.2011.08.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 07/29/2011] [Accepted: 08/07/2011] [Indexed: 10/17/2022]
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25
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Detection and identification of microorganisms in wine: a review of molecular techniques. J Ind Microbiol Biotechnol 2011; 38:1619-34. [DOI: 10.1007/s10295-011-1020-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 07/20/2011] [Indexed: 10/17/2022]
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26
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Applications of Fluorescence In Situ Hybridization in Diagnostic Microbiology. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Gray SR, Rawsthorne H, Dirks B, Phister TG. Detection and enumeration of Dekkera anomala in beer, cola, and cider using real-time PCR. Lett Appl Microbiol 2011; 52:352-9. [PMID: 21244454 DOI: 10.1111/j.1472-765x.2011.03008.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS In this article, a quantitative real-time PCR assay for detection and enumeration of the spoilage yeast Dekkera anomala in beer, cola, apple cider, and brewing wort is presented as an improvement upon existing detection methods, which are very time-consuming and not always accurate. METHODS AND RESULTS Primers were designed to exclude other organisms common in these beverages, and the assay was linear over 6 log units of cell concentrations. The addition of large amounts of non-target yeast DNA did not affect the efficiency of this assay. A standard curve of known DNA was established by plotting the C(t) values obtained from the QPCR against the log of plate counts on yeast peptone dextrose medium and unknowns showed exceptional correlation when tested against this standard curve. The assay was found to detect D. anomala at levels of 10-14 CFU ml⁻¹ in either cola or beer and at levels of 9·4-25·0 CFU ml⁻¹ in apple cider. The assay was also used to follow the growth of D. anomala in brewing wort. CONCLUSIONS The results indicate that real-time PCR is an effective tool for rapid, accurate detection and quantitation of D. anomala in beer, cola and apple cider. SIGNIFICANCE AND IMPACT OF THE STUDY This method gives a faster and more efficient technique to screen beer, cola, and cider samples and reduce spoilage by D. anomala. Faster screening may allow for significant reduction in economic loss because of reduced spoilage.
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Affiliation(s)
- S R Gray
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695-7624, USA
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Inácio J, Ludwig W, Spencer-Martins I, Fonseca A. Assessment of phylloplane yeasts on selected Mediterranean plants by FISH with group- and species-specific oligonucleotide probes. FEMS Microbiol Ecol 2010; 71:61-72. [PMID: 19817863 DOI: 10.1111/j.1574-6941.2009.00784.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
A previous culture-dependent survey of phylloplane yeasts from selected Mediterranean plants showed that a few species were present in high densities in almost all leaf samples, regardless of the plant type, location or sampling season. However, a few species appeared to be restricted to Cistus albidus leaves, namely Cryptococcus cistialbidi. Here, we describe a culture-independent FISH assay to detect and quantify whole yeast cells in leaf washings. After optimization, the technique was used to check the apparent association between C. albidus leaves and C. cistialbidi and the abundance and ubiquity of other basidiomycetous yeast species such as Erythrobasidium hasegawianum and Sporobolomyces spp. in leaf samples from this and other neighboring plants (Acer monspessulanum and Quercus faginea). No yeast cells were detected in Pistacia lentiscus leaf samples. We were also able to demonstrate that three phylloplane yeasts (C. cistialbidi, E. hasegawianum and Sporobolomyces spp.) appeared to be log-normally distributed among individual C. albidus leaves. The log-normal distribution has important implications for the quantification of phylloplane yeasts based on the washing and plating of bulk leaf samples, which will tend to overestimate the size of the respective populations and become an error source in yeast surveys or related biocontrol studies.
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Affiliation(s)
- João Inácio
- Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal.
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30
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Neu TR, Manz B, Volke F, Dynes JJ, Hitchcock AP, Lawrence JR. Advanced imaging techniques for assessment of structure, composition and function in biofilm systems. FEMS Microbiol Ecol 2010; 72:1-21. [PMID: 20180852 DOI: 10.1111/j.1574-6941.2010.00837.x] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Scientific imaging represents an important and accepted research tool for the analysis and understanding of complex natural systems. Apart from traditional microscopic techniques such as light and electron microscopy, new advanced techniques have been established including laser scanning microscopy (LSM), magnetic resonance imaging (MRI) and scanning transmission X-ray microscopy (STXM). These new techniques allow in situ analysis of the structure, composition, processes and dynamics of microbial communities. The three techniques open up quantitative analytical imaging possibilities that were, until a few years ago, impossible. The microscopic techniques represent powerful tools for examination of mixed environmental microbial communities usually encountered in the form of aggregates and films. As a consequence, LSM, MRI and STXM are being used in order to study complex microbial biofilm systems. This mini review provides a short outline of the more recent applications with the intention to stimulate new research and imaging approaches in microbiology.
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Affiliation(s)
- Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany.
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31
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Cerqueira L, Azevedo NF, Almeida C, Jardim T, Keevil CW, Vieira MJ. DNA mimics for the rapid identification of microorganisms by fluorescence in situ hybridization (FISH). Int J Mol Sci 2008; 9:1944-60. [PMID: 19325728 PMCID: PMC2635612 DOI: 10.3390/ijms9101944] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 09/24/2008] [Accepted: 10/06/2008] [Indexed: 12/23/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a well-established technique that is used for a variety of purposes, ranging from pathogen detection in clinical diagnostics to the determination of chromosomal stability in stem cell research. The key step of FISH involves the detection of a nucleic acid region and as such, DNA molecules have typically been used to probe for the sequences of interest. However, since the turn of the century, an increasing number of laboratories have started to move on to the more robust DNA mimics methods, most notably peptide and locked nucleic acids (PNA and LNA). In this review, we will cover the state-of-the-art of the different DNA mimics in regard to their application as efficient markers for the presence of individual microbial cells, and consider their potential advantages and pitfalls. Available PNA probes are then reassessed in terms of sensitivity and specificity using rRNA databases. In addition, we also attempt to predict the applicability of DNA mimics in well-known techniques attempting to detect in situ low number of copies of specific nucleic acid sequences such as catalyzed reporter deposition (CARD) and recognition of individual genes (RING) FISH.
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Affiliation(s)
- Laura Cerqueira
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal. E-Mails:
(L. C.);
(C. A.);
(T. J.);
(M. V.)
| | - Nuno F. Azevedo
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal. E-Mails:
(L. C.);
(C. A.);
(T. J.);
(M. V.)
- Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK. E-Mail:
(N. A.)
- Author to whom correspondence should be addressed; E-Mail:
; Tel. +351-253605413; Fax: +351-253678986
| | - Carina Almeida
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal. E-Mails:
(L. C.);
(C. A.);
(T. J.);
(M. V.)
- Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK. E-Mail:
(N. A.)
| | - Tatiana Jardim
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal. E-Mails:
(L. C.);
(C. A.);
(T. J.);
(M. V.)
| | - Charles William Keevil
- Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK. E-Mail:
(N. A.)
| | - Maria J. Vieira
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal. E-Mails:
(L. C.);
(C. A.);
(T. J.);
(M. V.)
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Suárez R, Suárez-Lepe J, Morata A, Calderón F. The production of ethylphenols in wine by yeasts of the genera Brettanomyces and Dekkera: A review. Food Chem 2007. [DOI: 10.1016/j.foodchem.2006.03.030] [Citation(s) in RCA: 230] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bottari B, Ercolini D, Gatti M, Neviani E. Application of FISH technology for microbiological analysis: current state and prospects. Appl Microbiol Biotechnol 2006; 73:485-94. [PMID: 17051413 DOI: 10.1007/s00253-006-0615-z] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 07/13/2006] [Accepted: 08/08/2006] [Indexed: 02/07/2023]
Abstract
In order to identify and quantify the microorganisms present in a certain ecosystem, it has become necessary to develop molecular methods avoiding cultivation, which allows to characterize only the countable part of the microorganisms in the sample, therefore losing the information related to the microbial component which presents a vitality condition, although it cannot duplicate in culture medium. In this context, one of the most used techniques is fluorescence in situ hybridization (FISH) with ribosomal RNA targeted oligonucleotide probes. Owing to its speed and sensitivity, this technique is considered a powerful tool for phylogenetic, ecological, diagnostic and environmental studies in microbiology. Through the use of species-specific probes, it is possible to identify different microorganisms in complex microbial communities, thus providing a solid support to the understanding of inter-species interaction. The knowledge of the composition and distribution of microorganisms in natural habitats can be interesting for ecological reasons in microbial ecology, and for safety and technological aspects in food microbiology. Methodological aspects, use of different probes and applications of FISH to microbial ecosystems are presented in this review.
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Affiliation(s)
- Benedetta Bottari
- Department of Genetic, Biology of Microorganisms, Anthropology, Evolution, University of Parma, via Usberti 11/A, 43100 Parma, Italy.
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Nisiotou AA, Gibson GR. Isolation of culturable yeasts from market wines and evaluation of the 5.8S-ITS rDNA sequence analysis for identification purposes. Lett Appl Microbiol 2006; 41:454-63. [PMID: 16305670 DOI: 10.1111/j.1472-765x.2005.01795.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To test the possibility that wines available in the marketplace may contain culturable yeasts and to evaluate the 5.8S-ITS rDNA sequence analysis as adequate means for the identification of isolates. METHODS AND RESULTS As a case study, typical Greek wines were surveyed. Sequence analysis of the 5.8S-ITS rDNA was tested for its robustness in species or strain identification. Sixteen isolates could be assigned into the species Brettanomyces bruxellensis, Saccharomyces cerevisiae and Rhodotorula pinicola, whereas four isolates could not be safely identified. B. bruxellensis was the dominant species present in house wines, while non-Saccharomyces sp. were viable in aged wines of high alcohol content. CONCLUSIONS Yeast population depends on postfermentation procedures or storage conditions. Although 5.8S-ITS rDNA sequence analysis is generally a rapid method to identify wine yeast isolates at the species level, or even below that, it may not be sufficient for some genera. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report to show that commercial wines may possess diverse and potentially harmful yeast populations. The knowledge of yeasts able to reside in this niche environment is essential towards integrated quality assurance programmes. For selected species, the 5.8S-ITS rDNA sequence analysis is a rapid and accurate means.
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Affiliation(s)
- A A Nisiotou
- Food Microbial Science Unit, School of Food Biosciences, The University of Reading, UK.
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Martorell P, Barata A, Malfeito-Ferreira M, Fernández-Espinar MT, Loureiro V, Querol A. Molecular typing of the yeast species Dekkera bruxellensis and Pichia guilliermondii recovered from wine related sources. Int J Food Microbiol 2006; 106:79-84. [PMID: 16229917 DOI: 10.1016/j.ijfoodmicro.2005.05.014] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2004] [Revised: 05/19/2005] [Accepted: 05/30/2005] [Indexed: 11/28/2022]
Abstract
A total of 63 strains of Dekkera bruxellensis and 32 strains of Pichia guilliermondii isolated from wine related environments were identified by restriction analysis of the 5.8S-ITS region of the rDNA. These strains were subjected to intraspecific discrimination using mtDNA restriction and RAPD-PCR analysis. The isolates identified as D. bruxellensis yielded 3 different molecular patterns of mtDNA restriction using the endonuclease HinfI. The pattern A was the most frequent (58 strains) among strains from different sources, regions and countries. Pattern B (4 strains) and C (one strain) were determined in isolates from Portuguese wines. The discrimination among the pattern A strains was achieved by a RAPD-PCR assay with 3 primers (OPA-2, OPA-3 and OPA-9). A total of 12 haplotypes were obtained with the combination of the patterns provided by the 3 OPAs. The pattern 2 was the most frequent and extensively distributed being found in strains from different countries and from different sources like wine, barrique wood and insects. The strains of P. guilliermondii were characterized with restriction of mtDNA using the endonuclease HinfI yielding 7 different restriction patterns. These patterns were associated with different efficiencies of 4-ethylphenol production. Patterns A to D corresponded to 19 strains producing low levels of 4-ethylphenol (<1 mg/l) while patterns F and G grouped 13 strains producing high levels of 4-ethylphenol (>50 mg/l), when grown in synthetic media supplemented with 100 mg/l of p-coumaric acid. The high degree of polymorphism observed shows that intraspecific typing is essential for accurate yeast dissemination studies in wine related environments.
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Affiliation(s)
- Patricia Martorell
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos (CSIC), P.O. Box 73, E-46100 Burjassot, València, Spain
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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: 0.8] [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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Brehm-Stecher BF, Hyldig-Nielsen JJ, Johnson EA. Design and evaluation of 16S rRNA-targeted peptide nucleic acid probes for whole-cell detection of members of the genus Listeria. Appl Environ Microbiol 2005; 71:5451-7. [PMID: 16151137 PMCID: PMC1214657 DOI: 10.1128/aem.71.9.5451-5457.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Six fluorescein-labeled peptide nucleic acid oligomers targeting Listeria-specific sequences on the 16S ribosomal subunit were evaluated for their abilities to hybridize to whole cells by fluorescence in situ hybridization (FISH). Four of these probes yielded weak or no fluorescent signals after hybridization and were not investigated further. The remaining two FISH-compatible probes, LisUn-3 and LisUn-11, were evaluated for their reactivities against 22 Listeria strains and 17 other bacterial strains belonging to 10 closely related genera. Hybridization with BacUni-1, a domain-specific eubacterial probe, was used as a positive control for target accessibility in both Listeria spp. and nontarget cells. RNase T1 treatment of select cell types was used to confirm that positive fluorescence responses were rRNA dependent and to examine the extent of nonspecific staining of nontarget cells. Both LisUn-3 and LisUn-11 yielded rapid, bright, and genus-specific hybridizations at probe concentrations of approximately 100 pmol ml(-1). LisUn-11 was the brightest probe and stained all six Listeria species. LisUn-3 hybridized with all Listeria spp. except for L. grayi, for which it had two mismatched bases. A simple ethanolic fixation yielded superior results with Listeria spp. compared to fixation in 10% buffered formalin and was applicable to all cell types studied. This study highlights the advantages of peptide nucleic acid probes for FISH-based detection of gram-positive bacteria and provides new tools for the rapid detection of Listeria spp. These probes may be useful for the routine monitoring of food production environments in support of efforts to control L. monocytogenes.
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Affiliation(s)
- Byron F Brehm-Stecher
- Department of Food Science and Human Nutrition, 2312 Food Sciences Building, Iowa State University, Ames, IA 50011, USA.
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Couto JA, Barbosa A, Hogg T. A simple cultural method for the presumptive detection of the yeasts Brettanomyces/Dekkera in wines. Lett Appl Microbiol 2005; 41:505-10. [PMID: 16305678 DOI: 10.1111/j.1472-765x.2005.01782.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS The development of a simple and reliable procedure, compatible with routine use in wineries, for the presumptive detection of Brettanomyces/Dekkera from wine and wine-environment samples. METHODS AND RESULTS The method of detection of these yeasts employs a selective enrichment medium. The medium contains glucose (10 g l(-1)) as carbon and energy source, cycloheximide (20 mg l(-1)) to prevent growth of Saccharomyces, chloramphenicol (200 mg l(-1)) to prevent growth of bacteria and p-coumaric acid (20 mg l(-1)) as the precursor for the production of 4-ethyl-phenol. After the inoculation with wine, the medium is monitored by visual inspection of turbidity and by periodic olfactive analysis. Contaminated wines will develop visible turbidity in the medium and will produce the 4-ethyl-phenol off-odour, which can be easily detected by smelling. CONCLUSIONS A selective enrichment liquid medium was developed to differentially promote the growth and activity of Brettanomyces/Dekkera. The method is simple to execute, employing a simple-to-prepare medium and a periodic olfactive detection. SIGNIFICANCE AND IMPACT OF THE STUDY The characteristics of the procedure make it particularly applicable in a wine-making environment thus presenting important advantages to the wine industry.
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Affiliation(s)
- J A Couto
- Escola Superior de Biotecnologia, Universidade Católica Portuguesa, R. Dr António Bernardino de Almeida, Porto.
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Nielsen PE. The many faces of PNA. Int J Pept Res Ther 2005. [DOI: 10.1007/s10989-005-4860-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
Peptide nucleic acids (PNA) are deoxyribonucleic acid (DNA) mimics with a pseudopeptide backbone. PNA is an extremely good structural mimic of DNA (or of ribonucleic acid [RNA]), and PNA oligomers are able to form very stable duplex structures with Watson-Crick complementary DNA and RNA (or PNA) oligomers, and they can also bind to targets in duplex DNA by helix invasion. Therefore, these molecules are of interest in many areas of chemistry, biology, and medicine, including drug discovery, genetic diagnostics, molecular recognition, and the origin of life. Recent progress in studies of PNA properties and applications is reviewed.
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Affiliation(s)
- Peter E Nielsen
- Center for Biomolecular Recognition, IMBG, The Panum Institute, University of Copenhagen, Blegdamsvej 3C, Copenhagen DK-2200N, Denmark.
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Delaherche A, Claisse O, Lonvaud-Funel A. Detection and quantification of Brettanomyces bruxellensis and 'ropy'Pediococcus damnosus strains in wine by real-time polymerase chain reaction. J Appl Microbiol 2004; 97:910-5. [PMID: 15479405 DOI: 10.1111/j.1365-2672.2004.02334.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS Brettanomyces bruxellensis is a well-known wine spoilage yeast that causes undesirable off-flavours. Likewise, glucan-producing strains of ropy Pediococcus damnosus are considered as spoilage micro-organisms because the synthesis of glucan leads to an unacceptable viscosity of wine. METHODS AND RESULTS We developed a real-time PCR method to detect and quantify these two spoilage micro-organisms in wine. It is based on specific primer pairs for amplification of target DNA, and includes a melting-curve analysis of PCR products as a confirmatory test. CONCLUSIONS The detection limit in wine was 10(4) CFU ml(-1) for B. bruxellensis and 40 CFU ml(-1) for ropy Pediococcus damnosus. The real-time PCR proved to be reliable for the early, sensitive detection and quantification of B. bruxellensis and ropy P. damnosus in wine. SIGNIFICANCE AND IMPACT OF THE STUDY The real-time PCR-based method described in this study provides a new tool for monitoring spoilage micro-organisms in wine. Time-consuming culture and colony isolation steps are no longer needed, so winemakers can intervene before spoilage occurs.
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Affiliation(s)
- A Delaherche
- Faculté d'Oenologie, UMR Oenologie-Ampélologie, INRA-Université Victor Segalen Bordeaux, France
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Comitini F, Ingeniis De J, Pepe L, Mannazzu I, Ciani M. Pichia anomalaandKluyveromyces wickerhamiikiller toxins as new tools againstDekkera/Brettanomycesspoilage yeasts. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09761.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Cocolin L, Rantsiou K, Iacumin L, Zironi R, Comi G. Molecular detection and identification of Brettanomyces/Dekkera bruxellensis and Brettanomyces/Dekkera anomalus in spoiled wines. Appl Environ Microbiol 2004; 70:1347-55. [PMID: 15006752 PMCID: PMC368351 DOI: 10.1128/aem.70.3.1347-1355.2004] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this paper we describe the development of a PCR protocol to specifically detect Brettanomyces bruxellensis and B. anomalus. Primers DB90F and DB394R, targeting the D1-D2 loop of the 26S rRNA gene, were able to produce amplicons only when the DNA from these two species were used. No amplification product was obtained when DNA from other Brettanomyces spp. or wine yeasts were used as the templates. The 305-bp product was subjected to restriction enzyme analysis with DdeI to differentiate between B. bruxellensis and B. anomalus, and each species could be identified on the basis of the different restriction profiles. After optimization of the method by using strains from international collections, wine isolates were tested with the method proposed. Total agreement between traditional identification and molecular identification was observed. The protocol developed was also used for direct detection of B. bruxellensis and B. anomalus in wines suspected to be spoiled by Brettanomyces spp. Application of culture-based and molecular methods led us to the conclusion that 8 of 12 samples were spoiled by B. bruxellensis. Results based on the application of molecular methods suggested that two of the eight positive samples had been infected more recently, since specific signals were obtained at both the DNA and RNA levels.
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Affiliation(s)
- Luca Cocolin
- Dipartimento Scienze degli Alimenti, Università degli studi di Udine, 33100 Udine, Italy.
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Phister TG, Mills DA. Real-time PCR assay for detection and enumeration of Dekkera bruxellensis in wine. Appl Environ Microbiol 2004; 69:7430-4. [PMID: 14660395 PMCID: PMC310000 DOI: 10.1128/aem.69.12.7430-7434.2003] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Traditional methods to detect the spoilage yeast Dekkera bruxellensis from wine involve lengthy enrichments. To overcome this difficulty, we developed a quantitative real-time PCR method to directly detect and enumerate D. bruxellensis in wine. Specific PCR primers to D. bruxellensis were designed to the 26S rRNA gene, and nontarget yeast and bacteria common to the winery environment were not amplified. The assay was linear over a range of cell concentrations (6 log units) and could detect as little as 1 cell per ml in wine. The addition of large amounts of nontarget yeasts did not impact the efficiency of the assay. This method will be helpful to identify possible routes of D. bruxellensis infection in winery environments. Moreover, the time involved in performing the assay (3 h) should enable winemakers to more quickly make wine processing decisions in order to reduce the threat of spoilage by D. bruxellensis.
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Affiliation(s)
- Trevor G Phister
- Department of Viticulture and Enology, University of California, Davis, California 95616, USA
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Identification of yeasts isolated from wine-related environments and capable of producing 4-ethylphenol. Food Microbiol 2003. [DOI: 10.1016/s0740-0020(02)00152-1] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Inácio J, Behrens S, Fuchs BM, Fonseca A, Spencer-Martins I, Amann R. In situ accessibility of Saccharomyces cerevisiae 26S rRNA to Cy3-labeled oligonucleotide probes comprising the D1 and D2 domains. Appl Environ Microbiol 2003; 69:2899-905. [PMID: 12732564 PMCID: PMC154520 DOI: 10.1128/aem.69.5.2899-2905.2003] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) has proven to be most useful for the identification of microorganisms. However, species-specific oligonucleotide probes often fail to give satisfactory results. Among the causes leading to low hybridization signals is the reduced accessibility of the targeted rRNA site to the oligonucleotide, mainly for structural reasons. In this study we used flow cytometry to determine whole-cell fluorescence intensities with a set of 32 Cy3-labeled oligonucleotide probes covering the full length of the D1 and D2 domains in the 26S rRNA of Saccharomyces cerevisiae PYCC 4455(T). The brightest signal was obtained with a probe complementary to positions 223 to 240. Almost half of the probes conferred a fluorescence intensity above 60% of the maximum, whereas only one probe could hardly detect the cells. The accessibility map based on the results obtained can be extrapolated to other yeasts, as shown experimentally with 27 additional species (14 ascomycetes and 13 basidiomycetes). This work contributes to a more rational design of species-specific probes for yeast identification and monitoring.
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Affiliation(s)
- João Inácio
- Centro de Recursos Microbiológicos, Biotechnology Unit, Faculty of Sciences and Technology, New University of Lisbon, 2829-516 Caparica, Portugal
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