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Cheng CY, Zhang MY, Niu YC, Zhang M, Geng YH, Deng H. Comparison of Fungal Genera Isolated from Cucumber Plants and Rhizosphere Soil by Using Various Cultural Media. J Fungi (Basel) 2023; 9:934. [PMID: 37755042 PMCID: PMC10532442 DOI: 10.3390/jof9090934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Plant endophytic fungi and rhizosphere soil fungi are often reported as biocontrol agents against plant pathogens or with plant growth promotion potential. Four treatments were performed in field and greenhouse experiments where cucumber plants were inoculated with Trichoderma harzianum and Fusarium oxysporum in 2022. The roots, stems and leaves of cucumber plants and their rhizosphere soil were collected twice individually from the field and greenhouse for isolation of cucumber endophytic and rhizosphere soil fungi. All fungal strains were identified through sequence similarity of the ITS1-5.8s-ITS2 rDNA region. The potato dextrose agar (PDA) media yielded the highest number of genera isolated from cucumber plants, rhizosphere soil and both compared to other media. There were no significant differences among the four media for the isolation of all cucumber endophytic fungi. However, in the roots, the number of endophytic fungi isolated by MRBA was significantly higher than that isolated on malt extract agar (MEA), while in the stems, the number of fungi isolated with PDA was significantly higher than that isolated with Martin's rose bengal agar medium (MRBA). PDA had significantly higher isolation efficiency for the rhizosphere soil fungi than MRBA. The 28 fungal genera had high isolation efficiency, and the endophytic Trichoderma strains were significantly more isolated by MEA than those of MRBA. It is suggested that PDA can be used as a basic medium, and different cultural media can be considered for specific fungal genera.
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Affiliation(s)
- Chong-Yang Cheng
- Plant Protection College, Henan Agricultural University, No. 95 Wen-Hua Road, Zhengzhou 450002, China; (C.-Y.C.); (M.Z.)
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China; (M.-Y.Z.); (Y.-C.N.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China
| | - Ming-Yuan Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China; (M.-Y.Z.); (Y.-C.N.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China
| | - Yong-Chun Niu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China; (M.-Y.Z.); (Y.-C.N.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China
| | - Meng Zhang
- Plant Protection College, Henan Agricultural University, No. 95 Wen-Hua Road, Zhengzhou 450002, China; (C.-Y.C.); (M.Z.)
| | - Yue-Hua Geng
- Plant Protection College, Henan Agricultural University, No. 95 Wen-Hua Road, Zhengzhou 450002, China; (C.-Y.C.); (M.Z.)
| | - Hui Deng
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China; (M.-Y.Z.); (Y.-C.N.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, China
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Picozzi C, Clagnan E, Musatti A, Rollini M, Brusetti L. Characterization of Two Zymomonas mobilis Wild Strains and Analysis of Populations Dynamics during Their Leavening of Bread-like Doughs. Foods 2022; 11:foods11182768. [PMID: 36140896 PMCID: PMC9497783 DOI: 10.3390/foods11182768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 02/04/2023] Open
Abstract
Two Zymomonas mobilis wild strains (UMB478 and 479) isolated from water kefir were characterized for their biomass production levels and leavening performance when used as the inoculum of a real bread-like dough formulation. The obtained baked product would be consumable by people with adverse responses to Saccharomyces cerevisiae. In liquid cultures, the two strains reached similar biomass concentration (0.7 g CDW/L). UMB479 showed an interesting resistance to NaCl (MBC 30 g/L), that may be useful in the bakery sector. When inoculated in doughs, UMB479 produced the maximum dough volume (650 mL) after 5 h, glucose was almost consumed and 1 g/100 g of ethanol produced, +200% respective to UMB478. Using S. cerevisiae for comparison purposes, the dough doubled its volume fast, in only 2 h, but reached a final level of 575 mL, lower than that achieved by Z. mobilis. The analysis of bacterial and fungal population dynamics during dough leavening was performed through the Automated Ribosomal Intergenic Spacer Analysis (ARISA); doughs leavened by UMB479 showed an interesting decrease in fungal richness after leavening. S. cerevisiae, instead, created a more complex fungal community, similar before and after leavening. Results will pave the way for the use of Z. mobilis UMB479 in commercial yeast-free leavened products.
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Affiliation(s)
- Claudia Picozzi
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Elisa Clagnan
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, 39100 Bolzano, Italy
| | - Alida Musatti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Manuela Rollini
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
- Correspondence: ; Tel.: +39-0250319150
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, 39100 Bolzano, Italy
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Cardinali F, Foligni R, Ferrocino I, Harasym J, Orkusz A, Franciosa I, Milanović V, Garofalo C, Mannozzi C, Mozzon M, Cocolin L, Osimani A, Aquilanti L. Microbial diversity, morpho-textural characterization, and volatilome profile of the Portuguese thistle-curdled cheese Queijo da Beira Baixa PDO. Food Res Int 2022; 157:111481. [DOI: 10.1016/j.foodres.2022.111481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/02/2022] [Accepted: 06/04/2022] [Indexed: 11/04/2022]
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Kamilari E, Tomazou M, Antoniades A, Tsaltas D. High Throughput Sequencing Technologies as a New Toolbox for Deep Analysis, Characterization and Potentially Authentication of Protection Designation of Origin Cheeses? INTERNATIONAL JOURNAL OF FOOD SCIENCE 2019; 2019:5837301. [PMID: 31886165 PMCID: PMC6925717 DOI: 10.1155/2019/5837301] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 09/08/2019] [Accepted: 09/28/2019] [Indexed: 12/17/2022]
Abstract
Protected Designation of Origin (PDO) labeling of cheeses has been established by the European Union (EU) as a quality policy that assures the authenticity of a cheese produced in a specific region by applying traditional production methods. However, currently used scientific methods for differentiating and establishing PDO are limited in terms of time, cost, accuracy and their ability to identify through quantifiable methods PDO fraud. Cheese microbiome is a dynamic community that progressively changes throughout ripening, contributing via its metabolism to unique qualitative and sensorial characteristics that differentiate each cheese. High Throughput Sequencing (HTS) methodologies have enabled the more precise identification of the microbial communities developed in fermented cheeses, characterization of their population dynamics during the cheese ripening process, as well as their contribution to the development of specific organoleptic and physio-chemical characteristics. Therefore, their application may provide an additional tool to identify the key microbial species that contribute to PDO cheeses unique sensorial characteristics and to assist to define their typicityin order to distinguish them from various fraudulent products. Additionally, they may assist the cheese-makers to better evaluate the quality, as well as the safety of their products. In this structured literature review indications are provided on the potential for defining PDO enabling differentiating factors based on distinguishable microbial communities shaped throughout the ripening procedures associated to cheese sensorial characteristics, as revealed through metagenomic and metatranscriptomic studies. Conclusively, HTS applications, even though still underexploited, have the potential to demonstrate how the cheese microbiome can affect the ripening process and sensorial characteristics formation via the catabolism of the available nutrients and interplay with other compounds of the matrix and/or production of microbial origin metabolites and thus their further quality enhancement.
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Affiliation(s)
- Elena Kamilari
- Cyprus University of Technology, Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus
| | | | | | - Dimitrios Tsaltas
- Cyprus University of Technology, Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus
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Diversity and Biotechnological Potential of Xylan-Degrading Microorganisms from Orange Juice Processing Waste. WATER 2019. [DOI: 10.3390/w11020274] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The orange juice processing sector produces worldwide massive amounts of waste, which is characterized by high lignin, cellulose and hemicellulose content, and which exceeds 40% of the fruit’s dry weight (d.w.). In this work, the diversity and the biotechnological potential of xylan-degrading microbiota in orange juice processing waste were investigated through the implementation of an enrichment isolation strategy followed by enzyme assays for the determination of xylanolytic activities, and via next generation sequencing for microbial diversity identification. Intracellular rather than extracellular endo-1,4-β-xylanase activities were detected, indicating that peripheral cell-bound (surface) xylanases are involved in xylan hydrolysis by the examined microbial strains. Among the isolated microbial strains, bacterial isolates belonging to Pseudomonas psychrotolerans/P. oryzihabitans spectrum (99.9%/99.8% similarity, respectively) exhibited activities of 280 U/mg protein. In contrast, almost all microbial strains isolated exerted low extracellular 1,4-β-xylosidase activities (<5 U/mg protein), whereas no intracellular 1,4-β-xylosidase activities were detected for any of them. Illumina data showed the dominance of lactic and acetic acid bacteria and of the yeasts Hanseniaspora and Zygosaccharomyces. This is the first report on indigenous xylanolytic microbiota isolated from orange juice processing waste, possessing the biotechnological potential to serve as biocatalysts for citrus biomass valorization through the production of high-added value products and energy recovery.
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Fröhlich-Wyder MT, Arias-Roth E, Jakob E. Cheese yeasts. Yeast 2019; 36:129-141. [PMID: 30512214 DOI: 10.1002/yea.3368] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 01/01/2023] Open
Abstract
Numerous traditionally aged cheeses are surface ripened and develop a biofilm, known as the cheese rind, on their surfaces. The rind of such cheeses comprises a complex community of bacterial and fungal species that are jointly responsible for the typical characteristics of the various cheese varieties. Surface ripening starts directly after brining with the rapid colonization of the cheese surface by yeasts. The initially dominant yeasts are acid and salt-tolerant and are capable of metabolizing the lactate produced by the starter lactic acid bacteria and of producing NH3 from amino acids. Both processes cause the pH of the cheese surface to rise dramatically. This so-called deacidification process enables the establishment of a salt-tolerant, Gram-positive bacterial community that is less acid-tolerant. Over the past decade, knowledge of yeast diversity in cheeses has increased considerably. The yeast species with the highest prevalence on surface-ripened cheeses are Debaryomyces hansenii and Geotrichum candidum, but up to 30 species can be found. In the cheese core, only lactose-fermenting yeasts, such as Kluyveromyces marxianus, are expected to grow. Yeasts are recognized as having an indispensable impact on the development of cheese flavour and texture because of their deacidifying, proteolytic, and/or lipolytic activity. Yeasts are used not only in the production of surface-ripened cheeses but also as adjunct cultures in the vat milk in order to modify ripening behaviour and flavour of the cheese. However, yeasts may also be responsible for spoilage of cheese, causing early blowing, off-flavour, brown discolouration, and other visible alterations of cheese.
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7
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El Sheikha AF, Hu DM. Molecular techniques reveal more secrets of fermented foods. Crit Rev Food Sci Nutr 2018; 60:11-32. [DOI: 10.1080/10408398.2018.1506906] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Aly Farag El Sheikha
- Jiangxi Agricultural University, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Nanchang, China
- McMaster University, Department of Biology, Hamilton, Ontario, Canada
- Minufiya University, Faculty of Agriculture, Department of Food Science and Technology, Shibin El Kom, Minufiya Government, Egypt
| | - Dian-Ming Hu
- Jiangxi Agricultural University, Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, Nanchang, China
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Sun X, Lyu G, Luan Y, Zhao Z, Yang H, Su D. Analyses of microbial community of naturally homemade soybean pastes in Liaoning Province of China by Illumina Miseq Sequencing. Food Res Int 2018; 111:50-57. [PMID: 30007713 DOI: 10.1016/j.foodres.2018.05.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/16/2018] [Accepted: 05/03/2018] [Indexed: 01/09/2023]
Abstract
Traditional Chinese soybean pastes are homemade using natural fermentation and are quite common and popular in Liaoning Province. In this study, we investigated microbial diversity by collecting 23 samples from 10 cities and sequenced them using 2 × 300 bp Illumina Miseq Sequencing. 16S and ITS primers were used to amplify the V3-V4 region of the bacterial 16S rRNA gene and the ITS1 region of the fungal ITS rDNA gene, respectively. In total, 687,888 filtered bacterial sequences were obtained from nineteen samples and 1,091,649 filtered fungal sequences were obtained from twenty samples. Among the bacterial sequences, Firmicutes (74.77%), Proteobacteria (22.61%), and Actinobacteria (2.55%) were the predominant phyla, with Staphylococcus making up most of the Firmicutes. Among the fungal sequences, Ascomycota, Basidiomycota and Zygomycota accounted for 94.88%, 3.29% and 1.77%, respectively, while Glomeromycota and Chytridiomycota accounted for the remaining 0.06%. Most of the species from Ascomycota were unclassified Trichocomaceae and Debaryomyces, including 404578 and 187827 sequences, respectively. The microbial community in each sample was unique, most likely due to the geographical differences and external factors including the environment and manufacturing process during the fermentation. Soybean paste is the result of fermentation involving a great diversity of microorganisms, which include not only bacteria but also fungi.
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Affiliation(s)
- Xiaodong Sun
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China; College of Environment and Resources, Dalian Minzu University, Dalian 116600, China.
| | - Guozhong Lyu
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, China.
| | - Yushi Luan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China.
| | - Zhihui Zhao
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, China.
| | - Hong Yang
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, China.
| | - Dan Su
- College of Environment and Resources, Dalian Minzu University, Dalian 116600, China.
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Morgan HH, du Toit M, Setati ME. The Grapevine and Wine Microbiome: Insights from High-Throughput Amplicon Sequencing. Front Microbiol 2017; 8:820. [PMID: 28553266 PMCID: PMC5425579 DOI: 10.3389/fmicb.2017.00820] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 04/21/2017] [Indexed: 12/21/2022] Open
Abstract
From the time when microbial activity in wine fermentation was first demonstrated, the microbial ecology of the vineyard, grape, and wine has been extensively investigated using culture-based methods. However, the last 2 decades have been characterized by an important change in the approaches used for microbial examination, due to the introduction of DNA-based community fingerprinting methods such as DGGE, SSCP, T-RFLP, and ARISA. These approaches allowed for the exploration of microbial community structures without the need to cultivate, and have been extensively applied to decipher the microbial populations associated with the grapevine as well as the microbial dynamics throughout grape berry ripening and wine fermentation. These techniques are well-established for the rapid more sensitive profiling of microbial communities; however, they often do not provide direct taxonomic information and possess limited ability to detect the presence of rare taxa and taxa with low abundance. Consequently, the past 5 years have seen an upsurge in the application of high-throughput sequencing methods for the in-depth assessment of the grapevine and wine microbiome. Although a relatively new approach in wine sciences, these methods reveal a considerably greater diversity than previously reported, and identified several species that had not yet been reported. The aim of the current review is to highlight the contribution of high-throughput next generation sequencing and metagenomics approaches to vineyard microbial ecology especially unraveling the influence of vineyard management practices on microbial diversity.
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Affiliation(s)
- Horatio H Morgan
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
| | - Maret du Toit
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
| | - Mathabatha E Setati
- Department of Viticulture and Oenology, Institute for Wine Biotechnology, Stellenbosch UniversityStellenbosch, South Africa
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Abstract
The history of cheese manufacture is a "natural history" in which animals, microorganisms, and the environment interact to yield human food. Part of the fascination with cheese, both scientifically and culturally, stems from its ability to assume amazingly diverse flavors as a result of seemingly small details in preparation. In this review, we trace the roots of cheesemaking and its development by a variety of human cultures over centuries. Traditional cheesemakers observed empirically that certain environments and processes produced the best cheeses, unwittingly selecting for microorganisms with the best biochemical properties for developing desirable aromas and textures. The focus of this review is on the role of fungi in cheese ripening, with a particular emphasis on the yeast-like fungus Geotrichum candidum. Conditions that encourage the growth of problematic fungi such as Mucor and Scopulariopsis as well as Arachnida (cheese mites), and how such contaminants might be avoided, are discussed. Bethlehem cheese, a pressed, uncooked, semihard, Saint-Nectaire-type cheese manufactured in the United Sates without commercial strains of bacteria or fungi, was used as a model for the study of stable microbial succession during ripening in a natural environment. The appearance of fungi during a 60-day ripening period was documented using light and scanning electron microscopy, and it was shown to be remarkably reproducible and parallel to the course of ripening of authentic Saint-Nectaire cheese in the Auvergne region of France. Geotrichum candidum, Mucor, and Trichothecium roseum predominate the microbiotas of both cheese types. Geotrichum in particular was shown to have high diversity in different traditional cheese ripening environments, suggesting that traditional manufacturing techniques selected for particular fungi. This and other studies suggest that strain diversity arises in relation to the lore and history of the regions from which these types of cheeses arose.
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Porcellato D, Magri M, Narvhus J. Viable cells differentiation improves microbial dynamics study of fermented milks. Int Dairy J 2015. [DOI: 10.1016/j.idairyj.2015.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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High-throughput sequencing reveals microbial community diversity of Tibetan naturally fermented yak milk. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-014-1013-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Irlinger F, Layec S, Hélinck S, Dugat-Bony E. Cheese rind microbial communities: diversity, composition and origin. FEMS Microbiol Lett 2014; 362:1-11. [DOI: 10.1093/femsle/fnu015] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
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Hermet A, Mounier J, Keravec M, Vasseur V, Barbier G, Jany J. Application of capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) analysis for identification of fungal communities in cheese. Food Microbiol 2014; 41:82-90. [DOI: 10.1016/j.fm.2014.01.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 07/24/2013] [Accepted: 01/21/2014] [Indexed: 10/25/2022]
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Hymery N, Vasseur V, Coton M, Mounier J, Jany JL, Barbier G, Coton E. Filamentous Fungi and Mycotoxins in Cheese: A Review. Compr Rev Food Sci Food Saf 2014; 13:437-456. [PMID: 33412699 DOI: 10.1111/1541-4337.12069] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/12/2014] [Indexed: 12/01/2022]
Abstract
Important fungi growing on cheese include Penicillium, Aspergillus, Cladosporium, Geotrichum, Mucor, and Trichoderma. For some cheeses, such as Camembert, Roquefort, molds are intentionally added. However, some contaminating or technological fungal species have the potential to produce undesirable metabolites such as mycotoxins. The most hazardous mycotoxins found in cheese, ochratoxin A and aflatoxin M1, are produced by unwanted fungal species either via direct cheese contamination or indirect milk contamination (animal feed contamination), respectively. To date, no human food poisoning cases have been associated with contaminated cheese consumption. However, although some studies state that cheese is an unfavorable matrix for mycotoxin production; these metabolites are actually detected in cheeses at various concentrations. In this context, questions can be raised concerning mycotoxin production in cheese, the biotic and abiotic factors influencing their production, mycotoxin relative toxicity as well as the methods used for detection and quantification. This review emphasizes future challenges that need to be addressed by the scientific community, fungal culture manufacturers, and artisanal and industrial cheese producers.
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Affiliation(s)
- Nolwenn Hymery
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, ESIAB, Technopôle de Brest Iroise, Université de Brest, EA3882, 29280 Plouzané, France
| | - Valérie Vasseur
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, ESIAB, Technopôle de Brest Iroise, Université de Brest, EA3882, 29280 Plouzané, France
| | - Monika Coton
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, ESIAB, Technopôle de Brest Iroise, Université de Brest, EA3882, 29280 Plouzané, France
| | - Jérôme Mounier
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, ESIAB, Technopôle de Brest Iroise, Université de Brest, EA3882, 29280 Plouzané, France
| | - Jean-Luc Jany
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, ESIAB, Technopôle de Brest Iroise, Université de Brest, EA3882, 29280 Plouzané, France
| | - Georges Barbier
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, ESIAB, Technopôle de Brest Iroise, Université de Brest, EA3882, 29280 Plouzané, France
| | - Emmanuel Coton
- Laboratoire Universitaire de Biodiversité et d'Ecologie Microbienne, ESIAB, Technopôle de Brest Iroise, Université de Brest, EA3882, 29280 Plouzané, France
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Porcellato D, Brighton C, McMahon D, Oberg C, Lefevre M, Broadbent J, Steele J. Application of ARISA to assess the influence of salt content and cation type on microbiological diversity of Cheddar cheese. Lett Appl Microbiol 2014; 59:207-16. [DOI: 10.1111/lam.12263] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/21/2014] [Accepted: 04/04/2014] [Indexed: 01/09/2023]
Affiliation(s)
- D. Porcellato
- Department of Chemistry, Biotechnology and Food Science; Norwegian University of Life Science; Aas Norway
| | - C. Brighton
- Department of Nutrition, Dietetics, and Food Sciences, and Western Dairy Center; Utah State University; Logan UT USA
| | - D.J. McMahon
- Department of Nutrition, Dietetics, and Food Sciences, and Western Dairy Center; Utah State University; Logan UT USA
| | - C.J. Oberg
- Department of Nutrition, Dietetics, and Food Sciences, and Western Dairy Center; Utah State University; Logan UT USA
| | - M. Lefevre
- Department of Nutrition, Dietetics, and Food Sciences, and Western Dairy Center; Utah State University; Logan UT USA
| | - J.R. Broadbent
- Department of Nutrition, Dietetics, and Food Sciences, and Western Dairy Center; Utah State University; Logan UT USA
| | - J.L. Steele
- Department of Food Science; University of Wisconsin; Madison WI USA
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Montel MC, Buchin S, Mallet A, Delbes-Paus C, Vuitton DA, Desmasures N, Berthier F. Traditional cheeses: rich and diverse microbiota with associated benefits. Int J Food Microbiol 2014; 177:136-54. [PMID: 24642348 DOI: 10.1016/j.ijfoodmicro.2014.02.019] [Citation(s) in RCA: 356] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 02/17/2014] [Accepted: 02/22/2014] [Indexed: 11/26/2022]
Abstract
The risks and benefits of traditional cheeses, mainly raw milk cheeses, are rarely set out objectively, whence the recurrent confused debate over their pros and cons. This review starts by emphasizing the particularities of the microbiota in traditional cheeses. It then describes the sensory, hygiene, and possible health benefits associated with traditional cheeses. The microbial diversity underlying the benefits of raw milk cheese depends on both the milk microbiota and on traditional practices, including inoculation practices. Traditional know-how from farming to cheese processing helps to maintain both the richness of the microbiota in individual cheeses and the diversity between cheeses throughout processing. All in all more than 400 species of lactic acid bacteria, Gram and catalase-positive bacteria, Gram-negative bacteria, yeasts and moulds have been detected in raw milk. This biodiversity decreases in cheese cores, where a small number of lactic acid bacteria species are numerically dominant, but persists on the cheese surfaces, which harbour numerous species of bacteria, yeasts and moulds. Diversity between cheeses is due particularly to wide variations in the dynamics of the same species in different cheeses. Flavour is more intense and rich in raw milk cheeses than in processed ones. This is mainly because an abundant native microbiota can express in raw milk cheeses, which is not the case in cheeses made from pasteurized or microfiltered milk. Compared to commercial strains, indigenous lactic acid bacteria isolated from milk/cheese, and surface bacteria and yeasts isolated from traditional brines, were associated with more complex volatile profiles and higher scores for some sensorial attributes. The ability of traditional cheeses to combat pathogens is related more to native antipathogenic strains or microbial consortia than to natural non-microbial inhibitor(s) from milk. Quite different native microbiota can protect against Listeria monocytogenes in cheeses (in both core and surface) and on the wooden surfaces of traditional equipment. The inhibition seems to be associated with their qualitative and quantitative composition rather than with their degree of diversity. The inhibitory mechanisms are not well elucidated. Both cross-sectional and cohort studies have evidenced a strong association of raw-milk consumption with protection against allergic/atopic diseases; further studies are needed to determine whether such association extends to traditional raw-milk cheese consumption. In the future, the use of meta-omics methods should help to decipher how traditional cheese ecosystems form and function, opening the way to new methods of risk-benefit management from farm to ripened cheese.
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Affiliation(s)
| | - Solange Buchin
- INRA, UR342 Technologie et Analyses Laitières, F-39801 Poligny, France
| | - Adrien Mallet
- Normandie Univ, France; UNICAEN, ABTE, F-14032 Caen, France
| | - Céline Delbes-Paus
- INRA, Unité Recherches Fromagères, 20 Côte de Reyne, F-15000 Aurillac, France
| | - Dominique A Vuitton
- UNICAEN, ABTE, F-14032 Caen, France; EA3181/Université de Franche-Comté, 25030, Besançon, France
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Padovan ACB, Melo ASDA, Colombo AL. Systematic review and new insights into the molecular characterization of the Candida rugosa species complex. Fungal Genet Biol 2013; 61:33-41. [PMID: 24161727 DOI: 10.1016/j.fgb.2013.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 10/11/2013] [Accepted: 10/13/2013] [Indexed: 12/01/2022]
Abstract
Recently, Candida rugosa was characterized as a species complex comprising four taxa: C. rugosa sensu stricto, Candida pseudorugosa, Candida neorugosa and Candida mesorugosa. Although considered relatively rare, several clusters of candidemia due to C. rugosa complex had been reported presenting mortality rates close to 70%. In this work we discuss the systematization, phenotyping and molecular methods based on internal transcribed spacer region (ITS) sequencing and proteomic analyses for species identification, as well as clinical aspects of the C. rugosa complex. We performed a Bayesian phylogenetic analysis using 72 ITS sequences representative of C. rugosa complex isolates and related species within the genus. Biochemical, morphological and MALDI-TOF MS analyses were processed with C. rugosa complex type strains and related species isolates. We described that the phylogeny showed four distinct clades inferred with high posterior probabilities, corresponding to the four species within the C. rugosa complex, excluding C. pararugosa. Biochemical and morphological aspects distinguished only C. rugosa sensu stricto but were not sufficient to accurately identify species within the rest of the complex. Protein spectrum profiles differentiated all reference strains from different species analyzed. To our knowledge, we presented the first phylogenetic analysis using a large collection of ITS sequences as well as proteomic profiles generated from isolates of the C. rugosa complex and related species that can enlighten systematics, diagnostics and clinical research fields.
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Affiliation(s)
- Ana Carolina Barbosa Padovan
- Laboratório Especial de Micologia, Disciplina de Infectologia, Universidade Federal de São Paulo, São Paulo, SP, Brazil.
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19
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Sipiczki M. Pichia bruneiensis sp. nov., a biofilm-producing dimorphic yeast species isolated from flowers in Borneo. Int J Syst Evol Microbiol 2012; 62:3099-3104. [DOI: 10.1099/ijs.0.044974-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Taxonomic analysis of five yeast strains isolated from Hibiscus flowers in Brunei (Borneo) is described. The strains represent a dimorphic, biofilm-producing, anamorphic budding yeast species for which the name Pichia bruneiensis is proposed. P. bruneiensis alternates between yeast and pseudohyphal modes of growth. The pseudohyphae form biofilms on the surface of liquid media and penetrate into solid substrates. The sequences of the D1/D2 domains of the large subunit rRNA genes, the internal transcribed spacer (ITS) regions and the 18S rRNA genes were identical in the five strains and indicated a close phylogenetic relationship with teleomorph species of the genus Pichia. In a phylogenetic analysis of these sequences, the closest relative of the new species was Pichia fermentans (6 % nucleotide substitutions and indels in the D1/D2 domain). The type strain is 11-485T and has been deposited in the Centralbureau voor Schimmelcultures (Utrecht, the Netherlands) as CBS 12611T, the National Collection of Agricultural and Industrial Micro-organisms (Budapest, Hungary) as NCAIM Y.02019T and the Culture Collection of Yeasts (Bratislava, Slovakia) as CCY 29-189-1T. Mycobank no. MB800537.
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Affiliation(s)
- Matthias Sipiczki
- Department of Genetics and Applied Microbiology, University of Debrecen, 4032 Debrecen, Hungary
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20
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Panelli S, Buffoni JN, Bonacina C, Feligini M. Identification of moulds from the Taleggio cheese environment by the use of DNA barcodes. Food Control 2012. [DOI: 10.1016/j.foodcont.2012.05.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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22
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Biodiversity in Oscypek, a traditional Polish cheese, determined by culture-dependent and -independent approaches. Appl Environ Microbiol 2012; 78:1890-8. [PMID: 22247135 DOI: 10.1128/aem.06081-11] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Oscypek is a traditional Polish scalded-smoked cheese, with a protected-designation-of-origin (PDO) status, manufactured from raw sheep's milk without starter cultures in the Tatra Mountains region of Poland. This study was undertaken in order to gain insight into the microbiota that develops and evolves during the manufacture and ripening stages of Oscypek. To this end, we made use of both culturing and the culture-independent methods of PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing of 16S rRNA gene amplicons. The culture-dependent technique and PCR-DGGE fingerprinting detected the predominant microorganisms in traditional Oscypek, whereas the next-generation sequencing technique (454 pyrosequencing) revealed greater bacterial diversity. Besides members of the most abundant bacterial genera in dairy products, e.g., Lactococcus, Lactobacillus, Leuconostoc, Streptococcus, and Enterococcus, identified by all three methods, other, subdominant bacteria belonging to the families Bifidobacteriaceae and Moraxellaceae (mostly Enhydrobacter), as well as various minor bacteria, were identified by pyrosequencing. The presence of bifidobacterial sequences in a cheese system is reported for the first time. In addition to bacteria, a great diversity of yeast species was demonstrated in Oscypek by the PCR-DGGE method. Culturing methods enabled the determination of a number of viable microorganisms from different microbial groups and their isolation for potential future applications in specific cheese starter cultures.
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Alper I, Frenette M, Labrie S. Ribosomal DNA polymorphisms in the yeast Geotrichum candidum. Fungal Biol 2011; 115:1259-69. [PMID: 22115445 DOI: 10.1016/j.funbio.2011.09.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 09/08/2011] [Accepted: 09/10/2011] [Indexed: 10/17/2022]
Abstract
The dimorphic yeast Geotrichum candidum (teleomorph: Galactomyces candidus) is commonly used to inoculate washed-rind and bloomy-rind cheeses. However, little is known about the phylogenetic lineage of this microorganism. We have sequenced the complete 18S, 5.8S, 26S ribosomal RNA genes and their internal transcribed spacers (ITS1) and ITS2 regions (5126 nucleotides) from 18 G. candidum strains from various environmental niches, with a focus on dairy strains. Multiple sequence alignments revealed the presence of 60 polymorphic sites, which is generally unusual for ribosomal DNA (rDNA) within a given species because of the concerted evolution mechanism. This mechanism drives genetic homogenization to prevent the divergent evolution of rDNA copies within individuals. While the polymorphisms observed were mainly substitutions, one insertion/deletion (indel) polymorphism was detected in ITS1. No polymorphic sites were detected downstream from this indel site, that is, in 5.8S and ITS2. More surprisingly, many sequence electrophoregrams generated during the sequencing of the rDNA had dual peaks, suggesting that many individuals exhibited intragenomic rDNA variability. The ITS1-5.8S-ITS2 regions of four strains were cloned. The sequence analysis of 68 clones revealed 32 different ITS1-5.8S-ITS2 variants within these four strains. Depending on the strain, from four to twelve variants were detected, indicating that multiple rDNA copies were present in the genomes of these G. candidum strains. These results contribute to the debate concerning the use of the ITS region for barcoding fungi and suggest that community profiling techniques based on rDNA should be used with caution.
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Affiliation(s)
- Iraz Alper
- Nutraceuticals and Functional Foods Institute, STELA Dairy Research Centre, Department of Food Sciences and Nutrition, Université Laval, Quebec City, QC, Canada G1V 0A6
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Ndoye B, Rasolofo EA, LaPointe G, Roy D. A review of the molecular approaches to investigate the diversity and activity of cheese microbiota. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s13594-011-0031-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Filteau M, Lagacé L, LaPointe G, Roy D. Correlation of maple sap composition with bacterial and fungal communities determined by multiplex automated ribosomal intergenic spacer analysis (MARISA). Food Microbiol 2011; 28:980-9. [PMID: 21569942 DOI: 10.1016/j.fm.2011.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 01/19/2011] [Accepted: 01/25/2011] [Indexed: 10/18/2022]
Abstract
During collection, maple sap is contaminated by bacteria and fungi that subsequently colonize the tubing system. The bacterial microbiota has been more characterized than the fungal microbiota, but the impact of both components on maple sap quality remains unclear. This study focused on identifying bacterial and fungal members of maple sap and correlating microbiota composition with maple sap properties. A multiplex automated ribosomal intergenic spacer analysis (MARISA) method was developed to presumptively identify bacterial and fungal members of maple sap samples collected from 19 production sites during the tapping period. Results indicate that the fungal community of maple sap is mainly composed of yeast related to Mrakia sp., Mrakiella sp., Guehomyces pullulans, Cryptococcus victoriae and Williopsis saturnus. Mrakia, Mrakiella and Guehomyces peaks were identified in samples of all production sites and can be considered dominant and stable members of the fungal microbiota of maple sap. A multivariate analysis based on MARISA profiles and maple sap chemical composition data showed correlations between Candida sake, Janthinobacterium lividum, Williopsis sp., Leuconostoc mesenteroides, Mrakia sp., Rhodococcus sp., Pseudomonas tolaasii, G. pullulans and maple sap composition at different flow periods. This study provides new insights on the relationship between microbial community and maple sap quality.
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Affiliation(s)
- Marie Filteau
- Institut des Nutraceutiques et Aliments Fonctionnels, Département des Sciences des Aliments et de Nutrition, Université Laval, 2440 Boul. Hochelaga QC G1 V 0A6, Canada
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