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Aguiar-Cervera J, Visinoni F, Zhang P, Hollywood K, Vrhovsek U, Severn O, Delneri D. Effect of Hanseniaspora vineae and Saccharomyces cerevisiae co-fermentations on aroma compound production in beer. Food Microbiol 2024; 123:104585. [PMID: 39038891 DOI: 10.1016/j.fm.2024.104585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 06/07/2024] [Accepted: 06/16/2024] [Indexed: 07/24/2024]
Abstract
In recent years, the boom of the craft beer industry refocused the biotech interest from ethanol production to diversification of beer aroma profiles. This study analyses the fermentative phenotype of a collection of non-conventional yeasts and examines their role in creating new flavours, particularly through co-fermentation with industrial Saccharomyces cerevisiae. High-throughput solid and liquid media fitness screening compared the ability of eight Saccharomyces and four non-Saccharomyces yeast strains to grow in wort. We determined the volatile profile of these yeast strains and found that Hanseniaspora vineae displayed a particularly high production of the desirable aroma compounds ethyl acetate and 2-phenethyl acetate. Given that H. vineae on its own can't ferment maltose and maltotriose, we carried out mixed wort co-fermentations with a S. cerevisiae brewing strain at different ratios. The two yeast strains were able to co-exist throughout the experiment, regardless of their initial inoculum, and the increase in the production of the esters observed in the H. vineae monoculture was maintained, alongside with a high ethanol production. Moreover, different inoculum ratios yielded different aroma profiles: the 50/50 S. cerevisiae/H. vineae ratio produced a more balanced profile, while the 10/90 ratio generated stronger floral aromas. Our findings show the potential of using different yeasts and different inoculum combinations to tailor the final aroma, thus offering new possibilities for a broader range of beer flavours and styles.
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Affiliation(s)
- Jose Aguiar-Cervera
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom; Singer Instruments Co. Ltd, Somerset, United Kingdom
| | - Federico Visinoni
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Penghan Zhang
- Foundation Edmund Mach, San Michele all' Adige, Trento, Italy
| | - Katherine Hollywood
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Urska Vrhovsek
- Foundation Edmund Mach, San Michele all' Adige, Trento, Italy
| | - Oliver Severn
- Singer Instruments Co. Ltd, Somerset, United Kingdom
| | - Daniela Delneri
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom.
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2
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Hays M. Genetic conflicts in budding yeast: The 2μ plasmid as a model selfish element. Semin Cell Dev Biol 2024; 161-162:31-41. [PMID: 38598944 DOI: 10.1016/j.semcdb.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
Antagonistic coevolution, arising from genetic conflict, can drive rapid evolution and biological innovation. Conflict can arise both between organisms and within genomes. This review focuses on budding yeasts as a model system for exploring intra- and inter-genomic genetic conflict, highlighting in particular the 2-micron (2μ) plasmid as a model selfish element. The 2μ is found widely in laboratory strains and industrial isolates of Saccharomyces cerevisiae and has long been known to cause host fitness defects. Nevertheless, the plasmid is frequently ignored in the context of genetic, fitness, and evolution studies. Here, I make a case for further exploring the evolutionary impact of the 2μ plasmid as well as other selfish elements of budding yeasts, discuss recent advances, and, finally, future directions for the field.
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Affiliation(s)
- Michelle Hays
- Department of Genetics, Stanford University, Stanford, CA, United States.
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3
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Spruijtenburg B, Meis JF, Verweij PE, de Groot T, Meijer EFJ. Short Tandem Repeat Genotyping of Medically Important Fungi: A Comprehensive Review of a Powerful Tool with Extensive Future Potential. Mycopathologia 2024; 189:72. [PMID: 39096450 PMCID: PMC11297828 DOI: 10.1007/s11046-024-00877-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 07/11/2024] [Indexed: 08/05/2024]
Abstract
Fungal infections pose an increasing threat to public health. New pathogens and changing epidemiology are a pronounced risk for nosocomial outbreaks. To investigate clonal transmission between patients and trace the source, genotyping is required. In the last decades, various typing assays have been developed and applied to different medically important fungal species. While these different typing methods will be briefly discussed, this review will focus on the development and application of short tandem repeat (STR) genotyping. This method relies on the amplification and comparison of highly variable STR markers between isolates. For most common fungal pathogens, STR schemes were developed and compared to other methods, like multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis. The pros and cons of STR typing as compared to the other methods are discussed, as well as the requirements for the development of a solid STR typing assay. The resolution of STR typing, in general, is higher than MLST and AFLP, with WGS SNP analysis being the gold standard when it comes to resolution. Although most modern laboratories are capable to perform STR typing, little progress has been made to standardize typing schemes. Allelic ladders, as developed for Aspergillus fumigatus, facilitate the comparison of STR results between laboratories and develop global typing databases. Overall, STR genotyping is an extremely powerful tool, often complimentary to whole genome sequencing. Crucial details for STR assay development, its applications and merit are discussed in this review.
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Affiliation(s)
- Bram Spruijtenburg
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jacques F Meis
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Cologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Excellence Center for Medical Mycology, Institute of Translational Research, University of Cologne, Cologne, Germany
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul E Verweij
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Theun de Groot
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, The Netherlands
| | - Eelco F J Meijer
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, The Netherlands.
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, The Netherlands.
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands.
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4
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Harrison MC, Ubbelohde EJ, LaBella AL, Opulente DA, Wolters JF, Zhou X, Shen XX, Groenewald M, Hittinger CT, Rokas A. Machine learning enables identification of an alternative yeast galactose utilization pathway. Proc Natl Acad Sci U S A 2024; 121:e2315314121. [PMID: 38669185 PMCID: PMC11067038 DOI: 10.1073/pnas.2315314121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 02/27/2024] [Indexed: 04/28/2024] Open
Abstract
How genomic differences contribute to phenotypic differences is a major question in biology. The recently characterized genomes, isolation environments, and qualitative patterns of growth on 122 sources and conditions of 1,154 strains from 1,049 fungal species (nearly all known) in the yeast subphylum Saccharomycotina provide a powerful, yet complex, dataset for addressing this question. We used a random forest algorithm trained on these genomic, metabolic, and environmental data to predict growth on several carbon sources with high accuracy. Known structural genes involved in assimilation of these sources and presence/absence patterns of growth in other sources were important features contributing to prediction accuracy. By further examining growth on galactose, we found that it can be predicted with high accuracy from either genomic (92.2%) or growth data (82.6%) but not from isolation environment data (65.6%). Prediction accuracy was even higher (93.3%) when we combined genomic and growth data. After the GALactose utilization genes, the most important feature for predicting growth on galactose was growth on galactitol, raising the hypothesis that several species in two orders, Serinales and Pichiales (containing the emerging pathogen Candida auris and the genus Ogataea, respectively), have an alternative galactose utilization pathway because they lack the GAL genes. Growth and biochemical assays confirmed that several of these species utilize galactose through an alternative oxidoreductive D-galactose pathway, rather than the canonical GAL pathway. Machine learning approaches are powerful for investigating the evolution of the yeast genotype-phenotype map, and their application will uncover novel biology, even in well-studied traits.
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Affiliation(s)
- Marie-Claire Harrison
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235
| | - Emily J Ubbelohde
- Laboratory of Genetics, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Abigail L LaBella
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28262
| | - Dana A Opulente
- Laboratory of Genetics, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
- Department of Biology, Villanova University, Villanova, PA 19085
| | - John F Wolters
- Laboratory of Genetics, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | | | - Chris Todd Hittinger
- Laboratory of Genetics, Department of Energy (DOE) Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235
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5
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Sánchez-Adriá IE, Sanmartín G, Prieto JA, Estruch F, Randez-Gil F. Sourdough Yeast Strains Exhibit Thermal Tolerance, High Fermentative Performance, and a Distinctive Aromatic Profile in Beer Wort. Foods 2024; 13:1059. [PMID: 38611363 PMCID: PMC11011504 DOI: 10.3390/foods13071059] [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: 02/27/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
The increasing popularity of home brewing and the fast evolution of craft beer companies have fuelled the interest in novel yeasts as the main actors diversifying the beer portfolio. Here, we have characterized the thermal tolerance and brewing-related features of two sourdough (SD) isolates of Saccharomyces cerevisiae, SDy01 and SDy02, at different temperatures, 20 and 37 °C, comparing them with commercial brew strains, AaB and kNB. The SD strains exhibited tolerance to the main brewing-related stress conditions and increased growth rates and lower lag phases than the reference beer strains at both temperatures. Consistent with this, SDy01 and SDy02 displayed higher fermentative activity in terms of sugar rate depletion and the release of metabolic by-products. Moreover, SDy01 and SDy02 brewing at 20 °C increased their total amount of volatile compounds (VOCs), in particular, their esters and carboxyl compounds, as compared to the reference AaB strain. In contrast, fermentation at 37 °C resulted in a drastic reduction in the number of VOCs in wort fermented with SD yeast, especially in its level of esters. In conclusion, our results stress the high fermentative performance of SD strains in beer wort and their ability to provide a complex and specific aromatic profile at a wide range of temperatures.
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Affiliation(s)
- Isabel E. Sánchez-Adriá
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980 Paterna (Valencia), Spain (J.A.P.)
| | - Gemma Sanmartín
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980 Paterna (Valencia), Spain (J.A.P.)
| | - Jose A. Prieto
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980 Paterna (Valencia), Spain (J.A.P.)
| | - Francisco Estruch
- Department of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, 46100 Burjassot (Valencia), Spain;
| | - Francisca Randez-Gil
- Department of Biotechnology, Instituto de Agroquímica y Tecnología de los Alimentos, Consejo Superior de Investigaciones Científicas, Avda. Agustín Escardino, 7, 46980 Paterna (Valencia), Spain (J.A.P.)
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6
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Flores-Cosío G, García-Béjar JA, Sandoval-Nuñez D, Amaya-Delgado L. Stress response and adaptation mechanisms in Kluyveromyces marxianus. ADVANCES IN APPLIED MICROBIOLOGY 2024; 126:27-62. [PMID: 38637106 DOI: 10.1016/bs.aambs.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Kluyveromyces marxianus is a non-Saccharomyces yeast that has gained importance due to its great potential to be used in the food and biotechnology industries. In general, K. marxianus is a known yeast for its ability to assimilate hexoses and pentoses; even this yeast can grow in disaccharides such as sucrose and lactose and polysaccharides such as agave fructans. Otherwise, K. marxianus is an excellent microorganism to produce metabolites of biotechnological interest, such as enzymes, ethanol, aroma compounds, organic acids, and single-cell proteins. However, several studies highlighted the metabolic trait variations among the K. marxianus strains, suggesting genetic diversity within the species that determines its metabolic functions; this diversity can be attributed to its high adaptation capacity against stressful environments. The outstanding metabolic characteristics of K. marxianus have motivated this yeast to be a study model to evaluate its easy adaptability to several environments. This chapter will discuss overview characteristics and applications of K. marxianus and recent insights into the stress response and adaptation mechanisms used by this non-Saccharomyces yeast.
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Affiliation(s)
- G Flores-Cosío
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Camino Arenero, Col. El Bajio, C.P., Zapopan Jalisco, A.C, Mexico
| | - J A García-Béjar
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Camino Arenero, Col. El Bajio, C.P., Zapopan Jalisco, A.C, Mexico
| | - D Sandoval-Nuñez
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Camino Arenero, Col. El Bajio, C.P., Zapopan Jalisco, A.C, Mexico
| | - L Amaya-Delgado
- Industrial Biotechnology Unit, Center for Research and Assistance in Technology and Design of the State of Jalisco, Camino Arenero, Col. El Bajio, C.P., Zapopan Jalisco, A.C, Mexico.
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7
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Abstract
For thousands of years, humans have enjoyed the novel flavors, increased shelf-life, and nutritional benefits that microbes provide in fermented foods and beverages. Recent sequencing surveys of ferments have mapped patterns of microbial diversity across space, time, and production practices. But a mechanistic understanding of how fermented food microbiomes assemble has only recently begun to emerge. Using three foods as case studies (surface-ripened cheese, sourdough starters, and fermented vegetables), we use an ecological and evolutionary framework to identify how microbial communities assemble in ferments. By combining in situ sequencing surveys with in vitro models, we are beginning to understand how dispersal, selection, diversification, and drift generate the diversity of fermented food communities. Most food producers are unaware of the ecological processes occurring in their production environments, but the theory and models of ecology and evolution can provide new approaches for managing fermented food microbiomes, from farm to ferment.
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Affiliation(s)
- Nicolas L Louw
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
| | - Kasturi Lele
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
| | - Ruby Ye
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
| | - Collin B Edwards
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
- School of Biological Sciences, Washington State University, Vancouver, Washington, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA; , , , ,
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8
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Pietrafesa R, Siesto G, Tufariello M, Palombi L, Baiano A, Gerardi C, Braghieri A, Genovese F, Grieco F, Capece A. A multivariate approach to explore the volatolomic and sensory profiles of craft Italian Grape Ale beers produced with novel Saccharomyces cerevisiae strains. Front Microbiol 2023; 14:1234884. [PMID: 37577427 PMCID: PMC10414987 DOI: 10.3389/fmicb.2023.1234884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
This study investigated the influence of three Saccharomyces cerevisiae strains, selected from different matrices - CHE-3 (cherry), P4 (sourdough) and TA4-10 (grape must) - on characteristics of Italian Grape Ale (IGA) beers obtained at microbrewery scale. A multidisciplinary approach, combining results from analysis of chemical, volatile and organoleptic profiles of the beers, was adopted to underline the relationships between yeast starter and the quality of final products. Detection volatile organic compounds (VOCs) by Gas-Chromatography coupled with Mass Spectrometry (GC-MS) after extraction carried out by head-space micro-extraction (HS-SPME) revealed that the beer obtained by P4 strain differed from the others for its higher concentrations of esters, alcohols, and terpenes as confirmed by PCA (principal component analysis) and Cluster heatmap. Furthermore, sensorial analysis and consumer test showed that this sample differed from others by more pronounced notes of "fruity smell and floral" and "olfactory finesse," and it was the most appreciated beer for smell, taste, and overall quality. Conversely, CHE-3 was the sample with the lowest concentrations of the identified volatiles and, together TA4-10, showed the highest scores for smoked, yeast, malt, and hop notes. As far as we know, these are the first results on the application of indigenous S. cerevisiae strains in the production of craft IGA beers analyzed through a complex multivariate approach.
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Affiliation(s)
- Rocchina Pietrafesa
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Gabriella Siesto
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
- Spinoff StarFInn S.r.l.s., Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Maria Tufariello
- Consiglio Nazionale delle Ricerche, Istituto di Scienze delle Produzioni Alimentari (ISPA), Lecce, Italy
| | - Lorenzo Palombi
- Consiglio Nazionale delle Ricerche, Istituto di Fisica Applicata “Nello Carrara”, Firenze, Italy
| | - Antonietta Baiano
- Dipartimento di Scienze Agrarie, degli Alimenti e dell’Ambiente, Università di Foggia, Foggia, Italy
| | - Carmela Gerardi
- Consiglio Nazionale delle Ricerche, Istituto di Scienze delle Produzioni Alimentari (ISPA), Lecce, Italy
| | - Ada Braghieri
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Francesco Genovese
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
| | - Francesco Grieco
- Consiglio Nazionale delle Ricerche, Istituto di Scienze delle Produzioni Alimentari (ISPA), Lecce, Italy
| | - Angela Capece
- Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
- Spinoff StarFInn S.r.l.s., Scuola di Scienze Agrarie, Forestali, Alimentari ed Ambientali, Università degli Studi della Basilicata, Potenza, Italy
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9
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Groenewald M, Hittinger C, Bensch K, Opulente D, Shen XX, Li Y, Liu C, LaBella A, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe K, Rosa C, Boekhout T, Čadež N, éter G, Sampaio J, Lachance MA, Yurkov A, Daniel HM, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A. A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Stud Mycol 2023; 105:1-22. [PMID: 38895705 PMCID: PMC11182611 DOI: 10.3114/sim.2023.105.01] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/12/2023] [Indexed: 06/21/2024] Open
Abstract
The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named. Taxonomic novelties: New classes: Alloascoideomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Dipodascomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Lipomycetes M. Groenew., Hittinger, Opulente, A. Rokas, Pichiomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Sporopachydermiomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Trigonopsidomycetes M. Groenew., Hittinger, Opulente & A. Rokas. New orders: Alloascoideomycetes: Alloascoideales M. Groenew., Hittinger, Opulente & A. Rokas; Dipodascomycetes: Dipodascales M. Groenew., Hittinger, Opulente & A. Rokas; Lipomycetes: Lipomycetales M. Groenew., Hittinger, Opulente & A. Rokas; Pichiomycetes: Alaninales M. Groenew., Hittinger, Opulente & A. Rokas, Pichiales M. Groenew., Hittinger, Opulente & A. Rokas, Serinales M. Groenew., Hittinger, Opulente & A. Rokas; Saccharomycetes: Phaffomycetales M. Groenew., Hittinger, Opulente & A. Rokas, Saccharomycodales M. Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiomycetes: Sporopachydermiales M. Groenew., Hittinger, Opulente & A. Rokas; Trigonopsidomycetes: Trigonopsidales M. Groenew., Hittinger, Opulente & A. Rokas. New families: Alaninales: Pachysolenaceae M. Groenew., Hittinger, Opulente & A. Rokas; Pichiales: Pichiaceae M. Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiales: Sporopachydermiaceae M. Groenew., Hittinger, Opulente & A. Rokas. Citation: Groenewald M, Hittinger CT, Bensch K, Opulente DA, Shen X-X, Li Y, Liu C, LaBella AL, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe KH, Rosa CA, Boekhout T, Čadež N, Péter G, Sampaio JP, Lachance M-A, Yurkov AM, Daniel H-M, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A (2023). A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Studies in Mycology 105: 1-22. doi: 10.3114/sim.2023.105.01 This study is dedicated to the memory of Cletus P. Kurtzman (1938-2017), a pioneer of yeast taxonomy.
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Affiliation(s)
- M. Groenewald
- Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The
Netherlands;
| | - C.T. Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic
Science Innovation, DOE Great Lakes Bioenergy Research Center, J. F. Crow
Institute for the Study of Evolution, University of Wisconsin-Madison,
Madison, WI 53726, USA;
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The
Netherlands;
| | - D.A. Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic
Science Innovation, DOE Great Lakes Bioenergy Research Center, J. F. Crow
Institute for the Study of Evolution, University of Wisconsin-Madison,
Madison, WI 53726, USA;
- Department of Biology, Villanova University, Villanova, PA
19085;
| | - X.-X. Shen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou
310058, China;
| | - Y. Li
- Institute of Marine Science and Technology, Shandong University, Qingdao
266237, China;
| | - C. Liu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou
310058, China;
| | - A.L. LaBella
- Department of Bioinformatics and Genomics, The University of North
Carolina at Charlotte, Charlotte NC 28223, USA;
| | - X. Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease
Control, Integrative Microbiology Research Center, South China Agricultural
University, Guangzhou 510642, China;
| | - S. Limtong
- Department of Microbiology, Faculty of Science, Kasetsart University,
Bangkok 10900, Thailand;
| | - S. Jindamorakot
- Microbial Diversity and Utilization Research Team, National Center for
Genetic Engineering and Biotechnology, National Science and Technology
Development Agency, 113 Thailand Science Park, Khlong Nueng, Khlong Luang,
Pathum Thani 12120, Thailand;
| | - P. Gonçalves
- Associate Laboratory i4HB–Institute for Health and Bioeconomy,
NOVA School of Science and Technology, Universidade NOVA de Lisboa,
Caparica, Portugal;
- UCIBIO—Applied Molecular Biosciences Unit, Department of Life
Sciences, NOVA School of Science and Technology, Universidade NOVA de
Lisboa, Caparica, Portugal;
| | - V. Robert
- Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The
Netherlands;
| | - K.H. Wolfe
- Conway Institute and School of Medicine, University College Dublin,
Dublin 4, Ireland;
| | - C.A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de
Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil;
| | - T. Boekhout
- College of Sciences, King Saud University, Riyadh, Saudi
Arabia;
| | - N. Čadež
- Food Science and Technology Department, Biotechnical Faculty, University
of Ljubljana, Ljubljana, Slovenia;
| | - G. éter
- National Collection of Agricultural and Industrial Microorganisms,
Institute of Food Science and Technology, Hungarian University of
Agriculture and Life Sciences, H-1118, Budapest, Somlói út
14-16., Hungary;
| | - J.P. Sampaio
- UCIBIO, Departamento de Ciências da Vida, Faculdade de
Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516
Caparica, Portugal;
| | - M.-A. Lachance
- Department of Biology, University of Western Ontario, London, ON N6A
5B7, Canada;
| | - A.M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell
Cultures, 38124 Braunschweig, Germany;
| | - H.-M. Daniel
- BCCM/MUCL, Earth and Life Institute, Mycology Laboratory,
Université catholique de Louvain, 1348 Louvain-la-Neuve,
Belgium;
| | - M. Takashima
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI),
Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502,
Japan;
| | - K. Boundy-Mills
- Food Science and Technology, University of California Davis, Davis, CA,
95616, USA;
| | - D. Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera,
Instituto Andino Patagónico de Tecnologías Biológicas y
Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB,
Quintral 1250, San Carlos de Bariloche, 8400, Río Negro,
Argentina;
| | - K. Aoki
- Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI),
Tokyo University of Agriculture, Sakuragaoka, Setagaya, Tokyo 156-8502,
Japan;
| | - T. Sugita
- Laboratory of Microbiology, Meiji Pharmaceutical University, Noshio,
Kiyose, Tokyo 204-8588, Japan;
| | - A. Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative,
Vanderbilt University, Nashville, TN 37235, USA
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10
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Moimenta AR, Henriques D, Minebois R, Querol A, Balsa-Canto E. Modelling the physiological status of yeast during wine fermentation enables the prediction of secondary metabolism. Microb Biotechnol 2023; 16:847-861. [PMID: 36722662 PMCID: PMC10034642 DOI: 10.1111/1751-7915.14211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/28/2022] [Accepted: 01/01/2023] [Indexed: 02/02/2023] Open
Abstract
Saccharomyces non-cerevisiae yeasts are gaining momentum in wine fermentation due to their potential to reduce ethanol content and achieve attractive aroma profiles. However, the design of the fermentation process for new species requires intensive experimentation. The use of mechanistic models could automate process design, yet to date, most fermentation models have focused on primary metabolism. Therefore, these models do not provide insight into the production of secondary metabolites essential for wine quality, such as aromas. In this work, we formulate a continuous model that accounts for the physiological status of yeast, that is, exponential growth, growth under nitrogen starvation and transition to stationary or decay phases. To do so, we assumed that nitrogen starvation is associated with carbohydrate accumulation and the induction of a set of transcriptional changes associated with the stationary phase. The model accurately described the dynamics of time series data for biomass and primary and secondary metabolites obtained for various yeast species in single culture fermentations. We also used the proposed model to explore different process designs, showing how the addition of nitrogen could affect the aromatic profile of wine. This study underlines the potential of incorporating yeast physiology into batch fermentation modelling and provides a new means of automating process design.
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Affiliation(s)
- Artai R Moimenta
- Bioprocess and Biosystems Engineering, IIM-CSIC, Vigo, Spain
- Applied Mathematics II, University of Vigo, Vigo, Spain
| | - David Henriques
- Bioprocess and Biosystems Engineering, IIM-CSIC, Vigo, Spain
| | - Romain Minebois
- Systems Biology of Yeasts of Biotechnological Interest, IATA-CSIC, Paterna, Spain
| | - Amparo Querol
- Systems Biology of Yeasts of Biotechnological Interest, IATA-CSIC, Paterna, Spain
| | - Eva Balsa-Canto
- Bioprocess and Biosystems Engineering, IIM-CSIC, Vigo, Spain
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11
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De Guidi I, Legras JL, Galeote V, Sicard D. Yeast domestication in fermented food and beverages: past research and new avenues. Curr Opin Food Sci 2023. [DOI: 10.1016/j.cofs.2023.101032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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12
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Postigo V, O’Sullivan T, Elink Schuurman T, Arroyo T. Non-Conventional Yeast: Behavior under Pure Culture, Sequential and Aeration Conditions in Beer Fermentation. Foods 2022; 11:foods11223717. [PMID: 36429309 PMCID: PMC9689477 DOI: 10.3390/foods11223717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022] Open
Abstract
The use of wild yeasts, isolated from different environments, is becoming the most interesting option for the production of new beers. The objective of this study is to evaluate the potential of seven non-conventional yeast strains from five different species (Saccharomyces cerevisiae, Hanseniaspora guilliermondii, Metschnikowia pulcherrima, Torulaspora delbrueckii, and Zygosaccharomyces bailii) isolated from Madrid agriculture to produce type ale beer. Wild yeast strains were evaluated at laboratory and pilot plant scales under different fermentation conditions (pure, aerated, and sequential culture). Strain S. cerevisiae SafAle S-04 was used as a reference. Throughout the fermentation of beer, volatile compounds were determined by GC and residual sugars by HPLC, among other parameters. The yeast strains used for the fermentation in pure culture conditions were unable to ferment maltose and maltotriose (0.73-1.18% v/v of ethanol). The results of the study under aerated conditions showed varying levels of higher alcohol and ester concentrations. It should be noted that the strain CLI 1057 (S. cerevisiae) fermented maltose in the presence of oxygen (Kluyver effect). This strain also showed a high production of 4-vinyl guaiacol, making it suitable for producing beers with a phenolic profile. Finally, three strains (H. guilliermondii, Z. bailii, and T. delbrueckii) were evaluated in sequential culture together with commercial strain and found to improve the organoleptic characteristics of the brewed beer. These approaches offer the opportunity to add new product characteristics to the beers.
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Affiliation(s)
- Vanesa Postigo
- Department of Agri-Food, Madrid Institute for Rural, Agriculture and Food Research and Development (IMIDRA), El Encín, A-2, km 38.2, 28805 Alcalá de Henares, Spain
- Brewery La Cibeles, Petróleo 34, 28918 Leganés, Spain
| | - Tadhg O’Sullivan
- Heineken Supply Chain B.V., Burgemeester Smeetsweg 1, 2382 PH Zoeterwoude, The Netherlands
| | - Tom Elink Schuurman
- Heineken Supply Chain B.V., Burgemeester Smeetsweg 1, 2382 PH Zoeterwoude, The Netherlands
| | - Teresa Arroyo
- Department of Agri-Food, Madrid Institute for Rural, Agriculture and Food Research and Development (IMIDRA), El Encín, A-2, km 38.2, 28805 Alcalá de Henares, Spain
- Correspondence:
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13
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Li S, Zhang Y, Li X, Yin P, Wang T, Li Y, Zhang K, Sheng H, Lu S, Ji H, Fan Z, Li B. The Effect of the Ratio of Gamma Aminobutyric Acid-Producing Saccharomyces cerevisiae DL6–20 and Kluyveromyces marxianus B13–5 Addition on Cheese Quality. Front Microbiol 2022; 13:900394. [PMID: 35814701 PMCID: PMC9260010 DOI: 10.3389/fmicb.2022.900394] [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: 03/20/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Kazakh cheese is a traditional dairy product in Xinjiang, China. The function and potential probiotic characteristics of Saccharomyces cerevisiae DL6–20 and Kluyveromyces marxianus B13–5 in Kazakh cheese and its contribution to cheese fermentation was studied. In this study, the effect of the addition ratio of gamma aminobutyric acid (GABA)-producing S. cerevisiae DL6–20 and K. marxianus B13–5 on cheese quality was investigated. Cheeses were prepared by fermentations with a total of six treatments: comercial culture alone as control (CS), a combination with one yeast, either; K. marxianus B13–5 (CSM); S. cerevisiae DL6–20 (CSS); and three different proportions of this two yeasts (CSM:CSS 1:1, 1:2, 2:1). We measured the GABA content of cheese, as well as basic physical and chemical indicators, microbial content, free amino acid (FAA) content, texture, and flavor compound content. The total FAA content of mixed bacteria fermentation was higher than that of the single bacteria alone. The GABA content CSM:CSS 1:2 GABA content was 0.114 g/100 g, CSM:CSS 2:1 GABA content was 0.12 g/100 g, CSM:CSS1:1 content of GABA produced in the late ripening period of cheese was the highest, reaching 0.189 g/100 g and the number of LAB and yeasts in CSM:CSS 1:1 was higher than that of other cheeses. The mixed-strain fermentation generally produced cheeses with a higher protein content than that of the single-strain fermentation in the late stage of the maturation process, especially the protein content of CSM:CSS 1:1 during the ripening period, when the protein content was highest at day 50. CSM:CSS 1:1 had a low moisture content, making it easy to store. With the exception of water and protein content, there is no significant difference in other physical and chemical indicators. CSM:CSS 1:1 contributed to the formation of cheese texture. In addition, multivariate statistical analysis indicated that mixed-strain fermentation was beneficial to the production of cheese aroma, with the aroma production performance of CSM:CSS 1:2 and CSM:CSS 2:1 found to be better than that of CSM: CSS 1:1.
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Affiliation(s)
- Shan Li
- School of Food Science and Technology, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
- Henan Shuanghui Investment & Development Co., Ltd., Luohe, China
| | - Yan Zhang
- School of Food Science and Technology, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
- Zhoukou Vocational College of Arts and Science, Zhoukou, China
| | - Xu Li
- School of Food Science and Technology, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
- Guangdong Yikewei Biotech Co., Ltd., Guangzhou, China
| | - Pingping Yin
- School of Food Science and Technology, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Tengbin Wang
- School of Food Science and Technology, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
- Xinjiang Uygur Autonomous Region Analysis and Testing Research Institute, Xinjiang, China
| | - Yandie Li
- School of Food Science and Technology, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Kaili Zhang
- School of Food Science and Technology, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Huayang Sheng
- School of Food Science and Technology, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Shiling Lu
- School of Food Science and Technology, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Hua Ji
- School of Food Science and Technology, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Zhexin Fan
- School of Food Science and Technology, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
| | - Baokun Li
- School of Food Science and Technology, Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Shihezi University, Shihezi, China
- *Correspondence: Baokun Li,
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14
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Combined impacts of various plant derivative extracts and lactic acid bacteria on yeasts to develop a nutritional bar with antifungal properties. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101718] [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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15
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Motlhanka K, Lebani K, Garcia-Aloy M, Zhou N. Functional Characterization of khadi Yeasts Isolates for Selection of Starter Cultures. J Microbiol Biotechnol 2022; 32:307-316. [PMID: 34866127 PMCID: PMC9628858 DOI: 10.4014/jmb.2109.09003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/11/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022]
Abstract
Yeasts play an important role in spontaneous fermentation of traditional alcoholic beverages. Our previous study revealed that a mixed-consortia of both Saccharomyces and non-Saccharomyces yeasts were responsible for fermentation of khadi, a popular, non-standardized traditional beverage with an immense potential for commercialization in Botswana. Functional characterization of isolated fermenting yeasts from mixed consortia is an indispensable step towards the selection of potential starter cultures for commercialization of khadi. In this study, we report the characterization of 13 khadi isolates for the presence of brewing-relevant phenotypes such as their fermentative capacity, ability to utilize a range of carbon sources and their ability to withstand brewing-associated stresses, as a principal step towards selection of starter cultures. Khadi isolates such as Saccharomyces cerevisiae, Saccharomycodes ludwigii and Candida ethanolica showed good brewing credentials but Lachancea fermentati emerged as the isolate with the best brewing attributes with a potential as a starter culture. However, we were then prompted to investigate the potential of L. fermentati to influence the fruity aromatic flavor, characteristic of khadi. The aroma components of 18 khadi samples were extracted using headspace solid phase micro-extraction (HSSPME) and identified using a GC-MS. We detected esters as the majority of volatile compounds in khadi, typical of the aromatic signature of both khadi and L. fermentati associated fermentations. This work shows that L. fermentati has potential for commercial production of khadi.
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Affiliation(s)
- Koketso Motlhanka
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Central District, Palapye, Botswana
| | - Kebaneilwe Lebani
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Central District, Palapye, Botswana
| | - Mar Garcia-Aloy
- Metabolomics Unit, Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all’Adige, Italy
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Central District, Palapye, Botswana
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16
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Use of essential oils against foodborne spoilage yeasts: advantages and drawbacks. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Yue Q, Wang Z, Yu F, Tang X, Su L, Zhang S, Sun X, Li K, Zhao C, Zhao L. Changes in metabolite profiles and antioxidant and hypoglycemic activities of Laminaria japonica after fermentation. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Wang Y, Zhang C, Liu F, Jin Z, Xia X. Ecological succession and functional characteristics of lactic acid bacteria in traditional fermented foods. Crit Rev Food Sci Nutr 2022; 63:5841-5855. [PMID: 35014569 DOI: 10.1080/10408398.2021.2025035] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fermented foods are important parts of traditional food culture with a long history worldwide. Abundant nutritional materials and open fermentation contribute to the diversity of microorganisms, resulting in unique product quality and flavor. Lactic acid bacteria (LAB), as important part of traditional fermented foods, play a decisive role in the quality and safety of fermented foods. Reproduction and metabolic of microorganisms drive the food fermentation, and microbial interaction plays a major role in the fermentation process. Nowadays, LAB have attracted considerable interest due to their potentialities to add functional properties to certain foods or as supplements along with the research of gut microbiome. This review focuses on the characteristics of diversity and variability of LAB in traditional fermented foods, and describes the principal mechanisms involved in the flavor formation dominated by LAB. Moreover, microbial interactions and their mechanisms in fermented foods are presented. They provide a theoretical basis for exploiting LAB in fermented foods and improving the quality of traditional fermented foods. The traditional fermented food industry should face the challenge of equipment automation, green manufacturing, and quality control and safety in the production.
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Affiliation(s)
- Yingyu Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, China
| | - Chenhao Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, China
| | | | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, WuXi, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, WuXi, China
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19
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Spurley WJ, Fisher KJ, Langdon QK, Buh KV, Jarzyna M, Haase MAB, Sylvester K, Moriarty RV, Rodriguez D, Sheddan A, Wright S, Sorlie L, Hulfachor AB, Opulente DA, Hittinger CT. Substrate, temperature, and geographical patterns among nearly 2000 natural yeast isolates. Yeast 2022; 39:55-68. [PMID: 34741351 PMCID: PMC8881392 DOI: 10.1002/yea.3679] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/26/2021] [Indexed: 01/03/2023] Open
Abstract
Yeasts have broad importance as industrially and clinically relevant microbes and as powerful models for fundamental research, but we are only beginning to understand the roles yeasts play in natural ecosystems. Yeast ecology is often more difficult to study compared to other, more abundant microbes, but growing collections of natural yeast isolates are beginning to shed light on fundamental ecological questions. Here, we used environmental sampling and isolation to assemble a dataset of 1962 isolates collected from throughout the contiguous United States of America (USA) and Alaska, which were then used to uncover geographic patterns, along with substrate and temperature associations among yeast taxa. We found some taxa, including the common yeasts Torulaspora delbrueckii and Saccharomyces paradoxus, to be repeatedly isolated from multiple sampled regions of the USA, and we classify these as broadly distributed cosmopolitan yeasts. A number of yeast taxon-substrate associations were identified, some of which were novel and some of which support previously reported associations. Further, we found a strong effect of isolation temperature on the phyla of yeasts recovered, as well as for many species. We speculate that substrate and isolation temperature associations reflect the ecological diversity of and niche partitioning by yeast taxa.
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Affiliation(s)
| | | | | | - Kelly V. Buh
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Martin Jarzyna
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Max A. B. Haase
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53726, USA; Vilcek Institute of Graduate Biomedical Sciences and Institute for Systems Genetics, NYU Langone Health, New York, NY 10016, USA
| | - Kayla Sylvester
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53726, USA; Dept. of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Ryan V. Moriarty
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Daniel Rodriguez
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Angela Sheddan
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53726, USA; West Carroll High School, Savannah, IL 61074, USA
| | - Sarah Wright
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53726, USA; EAGLE School of Madison, Fitchburg, WI 53711, USA
| | - Lisa Sorlie
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53726, USA; School District of Bonduel, Bonduel, WI 54107, USA
| | - Amanda Beth Hulfachor
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI 53726, USA
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20
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Solieri L, Cassanelli S, Huff F, Barroso L, Branduardi P, Louis EJ, Morrissey JP. Insights on life cycle and cell identity regulatory circuits for unlocking genetic improvement in Zygosaccharomyces and Kluyveromyces yeasts. FEMS Yeast Res 2021; 21:foab058. [PMID: 34791177 PMCID: PMC8673824 DOI: 10.1093/femsyr/foab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/14/2021] [Indexed: 11/14/2022] Open
Abstract
Evolution has provided a vast diversity of yeasts that play fundamental roles in nature and society. This diversity is not limited to genotypically homogeneous species with natural interspecies hybrids and allodiploids that blur species boundaries frequently isolated. Thus, life cycle and the nature of breeding systems have profound effects on genome variation, shaping heterozygosity, genotype diversity and ploidy level. The apparent enrichment of hybrids in industry-related environments suggests that hybridization provides an adaptive route against stressors and creates interest in developing new hybrids for biotechnological uses. For example, in the Saccharomyces genus where regulatory circuits controlling cell identity, mating competence and meiosis commitment have been extensively studied, this body of knowledge is being used to combine interesting traits into synthetic F1 hybrids, to bypass F1 hybrid sterility and to dissect complex phenotypes by bulk segregant analysis. Although these aspects are less known in other industrially promising yeasts, advances in whole-genome sequencing and analysis are changing this and new insights are being gained, especially in the food-associated genera Zygosaccharomyces and Kluyveromyces. We discuss this new knowledge and highlight how deciphering cell identity circuits in these lineages will contribute significantly to identify the genetic determinants underpinning complex phenotypes and open new avenues for breeding programmes.
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Affiliation(s)
- Lisa Solieri
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Stefano Cassanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Amendola 2, 42122 Reggio Emilia, Italy
| | - Franziska Huff
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Liliane Barroso
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Piazza della Scienza, 2-20126 Milano, Italy
| | - Edward J Louis
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John P Morrissey
- School of Microbiology, APC Microbiome Ireland, Environmental Research Institute, University College Cork, Cork T12 K8AF, Ireland
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21
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Abstract
Exopolysaccharides (EPS) are biopolymers produced by many microorganisms, including some species of the genus Acetobacter, Bacillus, Fructobacillus, Leuconostoc, Lactobacillus, Lactiplantibacillus, Pediococcus, Pichia, Rhodotorula, Saccharomycodes, Schizosaccharomyces, and Sphingomonas, which have been reported in the microbiota of traditional fermented beverages. Dextran, levan, glucan, gellan, and cellulose, among others, are EPS produced by these genera. Extracellular biopolymers are responsible for contributing to specific characteristics to fermented products, such as modifying their organoleptic properties or contributing to biological activities. However, EPS can be easily found in the dairy industry, where they affect rheological properties in products such as yogurt or cheese, among others. Over the years, LAB has been recognized as good starter strains in spontaneous fermentation, as they can contribute beneficial properties to the final product in conjunction with yeasts. To the best our knowledge, several articles have reported that the EPS produced by LAB and yeasts possess many both biological and technological properties that can be influenced by many factors in which fermentation occurs. Therefore, this review presents traditional Mexican fermented beverages (tavern, tuba, sotol, and aguamiel) and relates them to the microbial EPS, which affect biological and techno-functional activities.
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22
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Lu S, Zheng F, Wen L, He Y, Wang D, Wu M, Wang B. Yeast engineering technologies and their applications to the food industry. FOOD BIOTECHNOL 2021. [DOI: 10.1080/08905436.2021.1942037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Siyan Lu
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Fei Zheng
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Liankui Wen
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Yang He
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Donghui Wang
- SBU of Agriculture, Sinochem Group Co., Ltd., Beijing, China
| | - Manyu Wu
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Bixiang Wang
- Department of Food Science and Engineering, Jilin Agricultural University, Changchun, China
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Liu Y, Lin Y, Guo Y, Wu F, Zhang Y, Qi X, Wang Z, Wang Q. Stress tolerance enhancement via SPT15 base editing in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:155. [PMID: 34229745 PMCID: PMC8259078 DOI: 10.1186/s13068-021-02005-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/26/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Saccharomyces cerevisiae is widely used in traditional brewing and modern fermentation industries to produce biofuels, chemicals and other bioproducts, but challenged by various harsh industrial conditions, such as hyperosmotic, thermal and ethanol stresses. Thus, its stress tolerance enhancement has been attracting broad interests. Recently, CRISPR/Cas-based genome editing technology offers unprecedented tools to explore genetic modifications and performance improvement of S. cerevisiae. RESULTS Here, we presented that the Target-AID (activation-induced cytidine deaminase) base editor of enabling C-to-T substitutions could be harnessed to generate in situ nucleotide changes on the S. cerevisiae genome, thereby introducing protein point mutations in cells. The general transcription factor gene SPT15 was targeted, and total 36 mutants with diversified stress tolerances were obtained. Among them, the 18 tolerant mutants against hyperosmotic, thermal and ethanol stresses showed more than 1.5-fold increases of fermentation capacities. These mutations were mainly enriched at the N-terminal region and the convex surface of the saddle-shaped structure of Spt15. Comparative transcriptome analysis of three most stress-tolerant (A140G, P169A and R238K) and two most stress-sensitive (S118L and L214V) mutants revealed common and distinctive impacted global transcription reprogramming and transcriptional regulatory hubs in response to stresses, and these five amino acid changes had different effects on the interactions of Spt15 with DNA and other proteins in the RNA Polymerase II transcription machinery according to protein structure alignment analysis. CONCLUSIONS Taken together, our results demonstrated that the Target-AID base editor provided a powerful tool for targeted in situ mutagenesis in S. cerevisiae and more potential targets of Spt15 residues for enhancing yeast stress tolerance.
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Affiliation(s)
- Yanfang Liu
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuping Lin
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yufeng Guo
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Fengli Wu
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Yuanyuan Zhang
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Xianni Qi
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Zhen Wang
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qinhong Wang
- CAS Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
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24
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Bágeľová Poláková S, Lichtner Ž, Szemes T, Smolejová M, Sulo P. Mitochondrial DNA duplication, recombination, and introgression during interspecific hybridization. Sci Rep 2021; 11:12726. [PMID: 34135414 PMCID: PMC8209160 DOI: 10.1038/s41598-021-92125-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/03/2021] [Indexed: 02/05/2023] Open
Abstract
mtDNA recombination events in yeasts are known, but altered mitochondrial genomes were not completed. Therefore, we analyzed recombined mtDNAs in six Saccharomyces cerevisiae × Saccharomyces paradoxus hybrids in detail. Assembled molecules contain mostly segments with variable length introgressed to other mtDNA. All recombination sites are in the vicinity of the mobile elements, introns in cox1, cob genes and free standing ORF1, ORF4. The transplaced regions involve co-converted proximal exon regions. Thus, these selfish elements are beneficial to the host if the mother molecule is challenged with another molecule for transmission to the progeny. They trigger mtDNA recombination ensuring the transfer of adjacent regions, into the progeny of recombinant molecules. The recombination of the large segments may result in mitotically stable duplication of several genes.
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Affiliation(s)
- Silvia Bágeľová Poláková
- grid.7634.60000000109409708Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Bratislava, 842 15 Slovakia ,grid.419303.c0000 0001 2180 9405Present Address: Department of Membrane Biochemistry, Centre of Biosciences, Slovak Academy of Sciences, Bratislava, 84005 Slovakia
| | - Žaneta Lichtner
- grid.7634.60000000109409708Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Bratislava, 842 15 Slovakia
| | - Tomáš Szemes
- grid.7634.60000000109409708Comenius University Science Park, Bratislava, 841 04 Slovakia ,grid.7634.60000000109409708Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, 842 15 Slovakia ,Geneton s.r.o., Galvaniho 7, Bratislava, 821 04 Slovakia
| | - Martina Smolejová
- grid.7634.60000000109409708Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Bratislava, 842 15 Slovakia
| | - Pavol Sulo
- grid.7634.60000000109409708Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, Bratislava, 842 15 Slovakia
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25
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Tu Y, Huang S, Chi C, Lu P, Chen L, Li L, Li X. Digestibility and structure changes of rice starch following co-fermentation of yeast and Lactobacillus strains. Int J Biol Macromol 2021; 184:530-537. [PMID: 34139245 DOI: 10.1016/j.ijbiomac.2021.06.069] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 05/30/2021] [Accepted: 06/09/2021] [Indexed: 10/21/2022]
Abstract
Rice is sometimes fermented with microorganisms to develop health-promoting foods, but the contribution of a short-term fermentation (a necessary step for fermented rice cake-preparation) to properties of rice starch is not resolved yet. The effects of microorganism fermentation with different amount of starter cultures on multi-scale structures and digestibility of rice starch were investigated. The amount of starter cultures significantly affected structures and digestibility of fermented starch. The fermentation with a lower amount of starter cultures induced starch degradation (corrosion of starch granules, reduction of lamellar orders and compactness, decrease in crystallinity, double helix, short ranger-ordered structures, and molar mass) and a slightly reassembly, which increased the content of slowly digestible starch (SDS). While, the fermentation produced more starch fractions with Mw between 0.60 × 107 g/mol and 1.50 × 107 g/mol as the amount of starter cultures increased, and these starch molecules tended to reassemble and form more ordered multi-scale structures including double helical and short range-ordered structures, starch lamellar orders and compactness, which elevated SDS content. The SDS content of fermented starchy foods could be improved via controlling starch reassembly and multi-scale ordered structures through modulating the amount of starter cultures during fermentation.
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Affiliation(s)
- Yuan Tu
- Ministry of Education Engineering Research Center of Starch and Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Shuangxia Huang
- Ministry of Education Engineering Research Center of Starch and Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Chengdeng Chi
- Ministry of Education Engineering Research Center of Starch and Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Ping Lu
- Ministry of Education Engineering Research Center of Starch and Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Ling Chen
- Ministry of Education Engineering Research Center of Starch and Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Lin Li
- Ministry of Education Engineering Research Center of Starch and Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Xiaoxi Li
- Ministry of Education Engineering Research Center of Starch and Protein Processing, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China.
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26
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LaBella AL, Opulente DA, Steenwyk JL, Hittinger CT, Rokas A. Signatures of optimal codon usage in metabolic genes inform budding yeast ecology. PLoS Biol 2021; 19:e3001185. [PMID: 33872297 PMCID: PMC8084343 DOI: 10.1371/journal.pbio.3001185] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 04/29/2021] [Accepted: 03/15/2021] [Indexed: 02/06/2023] Open
Abstract
Reverse ecology is the inference of ecological information from patterns of genomic variation. One rich, heretofore underutilized, source of ecologically relevant genomic information is codon optimality or adaptation. Bias toward codons that match the tRNA pool is robustly associated with high gene expression in diverse organisms, suggesting that codon optimization could be used in a reverse ecology framework to identify highly expressed, ecologically relevant genes. To test this hypothesis, we examined the relationship between optimal codon usage in the classic galactose metabolism (GAL) pathway and known ecological niches for 329 species of budding yeasts, a diverse subphylum of fungi. We find that optimal codon usage in the GAL pathway is positively correlated with quantitative growth on galactose, suggesting that GAL codon optimization reflects increased capacity to grow on galactose. Optimal codon usage in the GAL pathway is also positively correlated with human-associated ecological niches in yeasts of the CUG-Ser1 clade and with dairy-associated ecological niches in the family Saccharomycetaceae. For example, optimal codon usage of GAL genes is greater than 85% of all genes in the genome of the major human pathogen Candida albicans (CUG-Ser1 clade) and greater than 75% of genes in the genome of the dairy yeast Kluyveromyces lactis (family Saccharomycetaceae). We further find a correlation between optimization in the GALactose pathway genes and several genes associated with nutrient sensing and metabolism. This work suggests that codon optimization harbors information about the metabolic ecology of microbial eukaryotes. This information may be particularly useful for studying fungal dark matter-species that have yet to be cultured in the lab or have only been identified by genomic material.
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Affiliation(s)
- Abigail Leavitt LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Dana A. Opulente
- Department of Biology, Villanova University, Villanova, Pennsylvania, United States of America
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
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27
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Marco ML, Sanders ME, Gänzle M, Arrieta MC, Cotter PD, De Vuyst L, Hill C, Holzapfel W, Lebeer S, Merenstein D, Reid G, Wolfe BE, Hutkins R. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nat Rev Gastroenterol Hepatol 2021; 18:196-208. [PMID: 33398112 PMCID: PMC7925329 DOI: 10.1038/s41575-020-00390-5] [Citation(s) in RCA: 237] [Impact Index Per Article: 79.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2020] [Indexed: 02/07/2023]
Abstract
An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term 'fermented' led the panel to define fermented foods and beverages as "foods made through desired microbial growth and enzymatic conversions of food components". This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines.
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Affiliation(s)
- Maria L Marco
- Department of Food Science and Technology, University of California-Davis, Davis, CA, USA
| | - Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, Centennial, CO, USA
| | - Michael Gänzle
- University of Alberta, Department of Agricultural, Food and Nutritional Science, Edmonton, Canada
| | - Marie Claire Arrieta
- Department of Physiology and Pharmacology, International Microbiome Center, University of Calgary, Calgary, Canada
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- VistaMilk, Cork, Ireland
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Colin Hill
- APC Microbiome Ireland and School of Microbiology, University College Cork, Cork, Ireland
| | - Wilhelm Holzapfel
- Advanced Green Energy and Environment Institute, Handong Global University, Pohang, Gyeongbuk, South Korea
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Dan Merenstein
- Department of Family Medicine, Georgetown University, Washington, DC, USA
| | - Gregor Reid
- Lawson Health Research Institute, and Departments of Microbiology & Immunology and Surgery, University of Western Ontario, London, Ontario, Canada
| | | | - Robert Hutkins
- Department of Food Science and Technology, University of Nebraska - Lincoln, Lincoln, NE, USA.
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28
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Effect of yeasts on food quality and safety and possibilities of their inhibition. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2020.11.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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29
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Brewing Characteristics of the Maltotriose-Positive Yeast Zygotorulaspora florentina Isolated from Oak. BEVERAGES 2020. [DOI: 10.3390/beverages6040058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The use of wild yeasts in fermentation is becoming a viable option for the differentiation of beers. To achieve good fermentation rates and alcohol yields, however, such yeasts must have the ability to utilize the wort sugars maltose and maltotriose, a relatively rare trait amongst non-domesticated yeasts. Zygotorulaspora florentina is a species with the ability to utilize both sugars, and was evaluated here with respect to its brewing potential. The strain studied (VTT C-201041) was isolated from bark of an oak tree (Quercus robur) in Espoo, Finland. The fermentation performance of the strain was compared to that of two ale yeasts as well as the species type strain (VTT C-94199). Both Z. florentina strains fermented wort efficiently (apparent attenuation levels >77%). While the type strain had the highest yield, the Finnish strain produced more volatile aroma compounds. The species is capable of decarboxylating ferulic acid to produce the spice/clove-like compound 4-vinylguaiacol, which was present in beers at a concentration above the typical flavor threshold. The characteristic flavor of 4-vinylguaiacol was not however perceptible in taste trials, possibly due to the masking effect of other compounds. The potential of this species for industrial application is discussed, particularly in relation to its apparent ethanol sensitivity.
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30
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Magalhães F, Calton A, Heiniö RL, Gibson B. Frozen-dough baking potential of psychrotolerant Saccharomyces species and derived hybrids. Food Microbiol 2020; 94:103640. [PMID: 33279066 DOI: 10.1016/j.fm.2020.103640] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/21/2020] [Accepted: 09/03/2020] [Indexed: 12/14/2022]
Abstract
Despite Saccharomyces cerevisiae being a synonym for baker's yeast, the species does not perform well in all baking-related conditions. In particular, dough fermentation, or proofing, is compromised by the species' sensitivity to the low and freezing temperatures that are often used in modern bakeries. Here, screening trials that included representatives of all known Saccharomyces species, showed that S. cerevisiae was generally the most sensitive member of the genus with respect to cold and freezing conditions. We hypothesized therefore that the superior cold tolerance of the non-S. cerevisiae yeast would enable their use as frozen-dough baking strains. To test this, the different yeast species were incorporated into doughs, flash frozen and kept in a frozen state for 14 days. During the proofing stage, dough development was lower in doughs that had been frozen, relative to fresh doughs. This reduction in fermentation performance was however most pronounced with S. cerevisiae. The psychrotolerant yeasts S. eubayanus, S. jurei and S. arboricola showed a strong capacity for post-freeze proofing in terms of dough development and duration of lag phase prior to fermentation. The superior proofing power of these species resulted in breads that were significantly softer and less dense than those prepared with S. cerevisiae. A sensory panel could distinguish the S. cerevisiae and non-S. cerevisiae breads based on their physical properties, but aroma and taste were unaffected by the species employed. To further improve frozen dough baking properties, S. eubayanus, S. jurei and S. arboricola were crossed with baker's yeast through rare mating, and hybrids with improved proofing capacities in both fresh and frozen doughs relative to the parents were created. The use of S. jurei and S. arboricola in baking represents the first potential technological application of these species.
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Affiliation(s)
- Frederico Magalhães
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, FI-02044, VTT, Espoo, Finland.
| | - Alex Calton
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, FI-02044, VTT, Espoo, Finland
| | - Raija-Liisa Heiniö
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, FI-02044, VTT, Espoo, Finland
| | - Brian Gibson
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, P.O. Box 1000, FI-02044, VTT, Espoo, Finland
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Abstract
AbstractSaccharomyces paradoxus is commonly isolated from environmental samples in Northern Europe and North America, but is rarely found associated with fermentation. However, as novelty has become a selling point in beer markets, interest toward non-conventional and local yeasts is increasing. Here, we report the first comprehensive investigation of the brewing potential of the species. Eight wild strains of S. paradoxus were isolated from oak trees growing naturally in Finland, screened in a series of fermentation trials and the most promising strain was selected for lager beer brewing at pilot scale (40 l). Yeasts were evaluated according to their ability to utilize wort sugars, their production of flavour-active aroma volatiles, diacetyl and organic acids, and sensorial quality of beers produced. All strains could assimilate maltose but this occurred after a considerable lag phase. Once adapted, most wild strains reached attenuation rates close to 70%. Adaptation to maltose could be maintained by re-pitching and with appropriate handling of the adapted yeast. Fermentation at 15 °C with the best performing strain was completed in 17 days. Maltose was consumed as efficiently as with a reference lager yeast, but no maltotriose use was observed. Bottled beers were evaluated by a trained sensory panel, and were generally rated as good as, or better than, reference beers. S. paradoxus beers were considered full-bodied and had a relatively clean flavour profile despite the presence of the clove-like 4-vinyl guaiacol. In conclusion, S. paradoxus exhibits a number of traits relevant to brewing, and with appropriate handling could be applied industrially.
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32
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Cuvas-Limon RB, Nobre C, Cruz M, Rodriguez-Jasso RM, Ruíz HA, Loredo-Treviño A, Texeira JA, Belmares R. Spontaneously fermented traditional beverages as a source of bioactive compounds: an overview. Crit Rev Food Sci Nutr 2020; 61:2984-3006. [PMID: 32662286 DOI: 10.1080/10408398.2020.1791050] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Fermented food has been present throughout history, since fermentation not only helps preserving food, but also provides specific organoleptic characteristics typically associated to these foods. Most of the traditional fermented foods and artisanal beverages are produced by spontaneous generation, meaning no control of the microbiota, or the substrate used. Nevertheless, even not being standardized, they are an important source of bioactive compounds, such as antioxidant compounds, bioactive beeps, short chain fatty acids, amino acids, vitamins, and minerals. This review compiles a list of relevant traditional fermented beverages around the world, aiming to detail the fermentation process itself-including source of microorganisms, substrates, produced metabolites and the operational conditions involved. As well as to list the bioactive compounds present in each fermented food, together with their impact in the human health. Traditional fermented beverages from Mexico will be highlighted. These compounds are of high interest for the food, pharmaceutical and cosmetics industry. To scale-up the home fermentation processes, it is necessary to fully understand the microbiology and biochemistry behind these traditional products. The use of good quality raw materials with standardized methodologies and defined microorganisms, may improve and increase the production of the desirable bioactive compounds and open a market for novel functional products.
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Affiliation(s)
- R B Cuvas-Limon
- Food Research Department, School of Chemical Sciences, Autonomous University of Coahuila, Saltillo Coahuila, Saltillo, Coahuila, Mexico.,Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Clarisse Nobre
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Mario Cruz
- Department of Food Science and Technology, Antonio Narro Autonomous Agricultural University, Saltillo, Coahuila, Mexico
| | - Rosa M Rodriguez-Jasso
- Food Research Department, School of Chemical Sciences, Autonomous University of Coahuila, Saltillo Coahuila, Saltillo, Coahuila, Mexico
| | - Héctor A Ruíz
- Food Research Department, School of Chemical Sciences, Autonomous University of Coahuila, Saltillo Coahuila, Saltillo, Coahuila, Mexico
| | - Araceli Loredo-Treviño
- Food Research Department, School of Chemical Sciences, Autonomous University of Coahuila, Saltillo Coahuila, Saltillo, Coahuila, Mexico
| | - J A Texeira
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ruth Belmares
- Food Research Department, School of Chemical Sciences, Autonomous University of Coahuila, Saltillo Coahuila, Saltillo, Coahuila, Mexico
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Perpetuini G, Tittarelli F, Battistelli N, Suzzi G, Tofalo R. γ‐aminobutyric acid production by
Kluyveromyces marxianus
strains. J Appl Microbiol 2020; 129:1609-1619. [DOI: 10.1111/jam.14736] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 05/26/2020] [Accepted: 05/31/2020] [Indexed: 12/24/2022]
Affiliation(s)
- G. Perpetuini
- Faculty of BioScience and Technology for Food, Agriculture and Environment University of Teramo Teramo Italy
| | - F. Tittarelli
- Faculty of BioScience and Technology for Food, Agriculture and Environment University of Teramo Teramo Italy
| | - N. Battistelli
- Faculty of BioScience and Technology for Food, Agriculture and Environment University of Teramo Teramo Italy
| | - G. Suzzi
- Faculty of BioScience and Technology for Food, Agriculture and Environment University of Teramo Teramo Italy
| | - R. Tofalo
- Faculty of BioScience and Technology for Food, Agriculture and Environment University of Teramo Teramo Italy
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34
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Volatile Compound Screening Using HS-SPME-GC/MS on Saccharomyces eubayanus Strains under Low-Temperature Pilsner Wort Fermentation. Microorganisms 2020; 8:microorganisms8050755. [PMID: 32443420 PMCID: PMC7285299 DOI: 10.3390/microorganisms8050755] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/01/2022] Open
Abstract
The recent isolation of the yeast Saccharomyces eubayanus has opened new avenues in the brewing industry. Recent studies characterized the production of volatile compounds in a handful set of isolates, utilizing a limited set of internal standards, representing insufficient evidence into the ability of the species to produce new and diverse aromas in beer. Using Headspace solid-phase microextraction followed by gas chromatography-mass spectrometry (HS-SPME-GC-MS), we characterized for the first time the production of volatile compounds in 10 wild strains under fermentative brewing conditions and compared them to a commercial lager yeast. S. eubayanus produces a higher number of volatile compounds compared to lager yeast, including acetate and ethyl esters, together with higher alcohols and phenols. Many of the compounds identified in S. eubayanus are related to fruit and floral flavors, which were absent in the commercial lager yeast ferment. Interestingly, we found a significant strain × temperature interaction, in terms of the profiles of volatile compounds, where some strains produced significantly greater levels of esters and higher alcohols. In contrast, other isolates preferentially yielded phenols, depending on the fermentation temperature. This work demonstrates the profound fermentation product differences between different S. eubayanus strains, highlighting the enormous potential of this yeast to produce new styles of lager beers.
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35
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Aydın F, Özer G, Alkan M, Çakır İ. The utility of iPBS retrotransposons markers to analyze genetic variation in yeast. Int J Food Microbiol 2020; 325:108647. [PMID: 32361480 DOI: 10.1016/j.ijfoodmicro.2020.108647] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 10/24/2022]
Abstract
Yeasts are one of the main organisms in the food industry and effective components of many ecosystems. The method for identifying and detecting certain yeast species or strains is a crucial step for the food industry and should be simple, reliable, fast, and inexpensive. In our study, inter-priming binding sites (iPBS) retrotransposon marker system was employed to elucidate the genetic variability at intraspecies and interspecies levels among 112 yeast strains belonging to eight species previously obtained from fermented foods. The molecular identification of yeast strains was firstly confirmed by sequencing the D1/D2 domain of the 26S rRNA. The eight selected retrotransposon-based primers produced 278 bands, all of which were polymorphic with an average of 34.75 polymorphic fragments per primer. The averages of polymorphism information contents and the resolving power values for the iPBS marker system were 0.23 and 10.11, respectively. The genetic parameters within each yeast species obtained from iPBS markers were observed as; the percentage of polymorphic loci for each species ranging from 19.23% to 71.21%, Nei's gene diversity from 0.085 to 0.228, while Shannon's information index values ranging from 0.125 to 0.349. The value of gene flow (0.09) and genetic variation among the populations (0.85) showed higher genetic variation among the species. UPGMA analyses demonstrated considerable genetic variability in the yeast strains, clustered them according to their species, and revealed the intraspecific variation. Each of the selected iPBS primer provided enough species-discrimination. Present evaluations suggest the utility of iPBS marker system to estimate the genetic variation of yeast strains. This study is a preliminary point for further studies on the identification methodology, and population genetics of yeast species having importance in the food industry with iPBS markers.
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Affiliation(s)
- Furkan Aydın
- Department of Food Engineering, Faculty of Engineering, Aksaray University, Aksaray 68100, Turkey
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture and Natural Sciences, Bolu Abant Izzet Baysal University, Bolu 14030, Turkey.
| | - Mehtap Alkan
- Department of Plant Protection, Faculty of Agriculture and Natural Sciences, Bolu Abant Izzet Baysal University, Bolu 14030, Turkey
| | - İbrahim Çakır
- Department of Food Engineering, Faculty of Engineering, Bolu Abant Izzet Baysal University, Bolu 14030, Turkey
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Langdon QK, Peris D, Eizaguirre JI, Opulente DA, Buh KV, Sylvester K, Jarzyna M, Rodríguez ME, Lopes CA, Libkind D, Hittinger CT. Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybrids. PLoS Genet 2020; 16:e1008680. [PMID: 32251477 PMCID: PMC7162524 DOI: 10.1371/journal.pgen.1008680] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 04/16/2020] [Accepted: 02/18/2020] [Indexed: 01/19/2023] Open
Abstract
The wild, cold-adapted parent of hybrid lager-brewing yeasts, Saccharomyces eubayanus, has a complex and understudied natural history. The exploration of this diversity can be used both to develop new brewing applications and to enlighten our understanding of the dynamics of yeast evolution in the wild. Here, we integrate whole genome sequence and phenotypic data of 200 S. eubayanus strains, the largest collection known to date. S. eubayanus has a multilayered population structure, consisting of two major populations that are further structured into six subpopulations. Four of these subpopulations are found exclusively in the Patagonian region of South America; one is found predominantly in Patagonia and sparsely in Oceania and North America; and one is specific to the Holarctic ecozone. Plant host associations differed between subpopulations and between S. eubayanus and its sister species, Saccharomyces uvarum. S. eubayanus is most abundant and genetically diverse in northern Patagonia, where some locations harbor more genetic diversity than is found outside of South America, suggesting that northern Patagonia east of the Andes was a glacial refugium for this species. All but one subpopulation shows isolation-by-distance, and gene flow between subpopulations is low. However, there are strong signals of ancient and recent outcrossing, including two admixed lineages, one that is sympatric with and one that is mostly isolated from its parental populations. Using our extensive biogeographical data, we build a robust model that predicts all known and a handful of additional regions of the globe that are climatically suitable for S. eubayanus, including Europe where host accessibility and competitive exclusion by other Saccharomyces species may explain its continued elusiveness. We conclude that this industrially relevant species has rich natural diversity with many factors contributing to its complex distribution and natural history. The mysterious wild parent of hybrid-lager brewing yeasts, Saccharomyces eubayanus, has been known for less than 10 years. In this time, it has become clear that lager hybrids arose from a subpopulation that has only been isolated in Tibet and North Carolina, USA; but the global diversity of this species has been less explored. Here, we use whole genome sequencing data for 200 strains (174 newly sequenced) to investigate the genetic diversity and geographical distribution of S. eubayanus. We find that its extensive wild diversity is largely centered in northern Patagonia, which likely was a glacial refugium for this species as three of six subpopulations are endemic to this region. In contrast, S. eubayanus is rarely isolated outside of Patagonia. In North America, isolates are dominated by an invasive, near-clonal admixed lineage; the result of an outcrossing and migration event. All subpopulations are well-differentiated, with low gene flow between them. This genetic isolation of subpopulations could be due to ecological factors, such as plant host associations. With modeling, we find that many areas of the world are climatically suitable to S. eubayanus, including Europe, where it has never been isolated. We propose complex ancestries and rich ecologies underlie the global distribution and diversity of this elusive and industrially important species.
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Affiliation(s)
- Quinn K. Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
| | - David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Juan I. Eizaguirre
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) – CONICET / Universidad Nacional del Comahue, Quintral 1250, Bariloche, Argentina
| | - Dana A. Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
| | - Kelly V. Buh
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
| | - Kayla Sylvester
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
| | - Martin Jarzyna
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
| | - María E. Rodríguez
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, CONICET-UNCo), Neuquén, Argentina
| | - Christian A. Lopes
- Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas (PROBIEN, CONICET-UNCo), Neuquén, Argentina
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) – CONICET / Universidad Nacional del Comahue, Quintral 1250, Bariloche, Argentina
- * E-mail: (CTH); (DL)
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, United States of America
- * E-mail: (CTH); (DL)
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Gibson B, Dahabieh M, Krogerus K, Jouhten P, Magalhães F, Pereira R, Siewers V, Vidgren V. Adaptive Laboratory Evolution of Ale and Lager Yeasts for Improved Brewing Efficiency and Beer Quality. Annu Rev Food Sci Technol 2020; 11:23-44. [DOI: 10.1146/annurev-food-032519-051715] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Yeasts directly impact the efficiency of brewery fermentations as well as the character of the beers produced. In recent years, there has been renewed interest in yeast selection and development inspired by the demand to utilize resources more efficiently and the need to differentiate beers in a competitive market. Reviewed here are the different, non-genetically modified (GM) approaches that have been considered, including bioprospecting, hybridization, and adaptive laboratory evolution (ALE). Particular emphasis is placed on the latter, which represents an extension of the processes that have led to the domestication of strains already used in commercial breweries. ALE can be used to accentuate the positive traits of brewing yeast as well as temper some of the traits that are less desirable from a modern brewer's perspective. This method has the added advantage of being non-GM and therefore suitable for food and beverage production.
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Affiliation(s)
- B. Gibson
- VTT Technical Research Centre of Finland Ltd, FI-02044 Espoo, Finland
| | - M. Dahabieh
- Renaissance BioScience, Vancouver, British Columbia, Canada, V6T1Z3
| | - K. Krogerus
- VTT Technical Research Centre of Finland Ltd, FI-02044 Espoo, Finland
| | - P. Jouhten
- VTT Technical Research Centre of Finland Ltd, FI-02044 Espoo, Finland
| | - F. Magalhães
- VTT Technical Research Centre of Finland Ltd, FI-02044 Espoo, Finland
| | - R. Pereira
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - V. Siewers
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - V. Vidgren
- VTT Technical Research Centre of Finland Ltd, FI-02044 Espoo, Finland
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Libkind D, Peris D, Cubillos FA, Steenwyk JL, Opulente DA, Langdon QK, Rokas A, Hittinger CT. Into the wild: new yeast genomes from natural environments and new tools for their analysis. FEMS Yeast Res 2020; 20:foaa008. [PMID: 32009143 PMCID: PMC7067299 DOI: 10.1093/femsyr/foaa008] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 01/31/2020] [Indexed: 12/16/2022] Open
Abstract
Genomic studies of yeasts from the wild have increased considerably in the past few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp., which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here, we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.
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Affiliation(s)
- D Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC) – CONICET/Universidad Nacional del Comahue, Quintral 1250 (8400), Bariloche., Argentina
| | - D Peris
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology-CSIC, Calle Catedrático Dr. D. Agustin Escardino Benlloch n°7, 46980 Paterna, Valencia, Spain
| | - F A Cubillos
- Millennium Institute for Integrative Biology (iBio). General del Canto 51 (7500574), Santiago
- Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología. Alameda 3363 (9170002). Estación Central. Santiago, Chile
| | - J L Steenwyk
- Department of Biological Sciences, VU Station B#35-1634, Vanderbilt University, Nashville, TN 37235, USA
| | - D A Opulente
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, 1552 University Avenue, Madison, WI 53726-4084, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Avenue, Madison, I 53726-4084, Madison, WI, USA
| | - Q K Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, 1552 University Avenue, Madison, WI 53726-4084, USA
| | - A Rokas
- Department of Biological Sciences, VU Station B#35-1634, Vanderbilt University, Nashville, TN 37235, USA
| | - C T Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, 1552 University Avenue, Madison, WI 53726-4084, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Avenue, Madison, I 53726-4084, Madison, WI, USA
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39
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Parapouli M, Vasileiadis A, Afendra AS, Hatziloukas E. Saccharomyces cerevisiae and its industrial applications. AIMS Microbiol 2020; 6:1-31. [PMID: 32226912 PMCID: PMC7099199 DOI: 10.3934/microbiol.2020001] [Citation(s) in RCA: 166] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/19/2020] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces cerevisiae is the best studied eukaryote and a valuable tool for most aspects of basic research on eukaryotic organisms. This is due to its unicellular nature, which often simplifies matters, offering the combination of the facts that nearly all biological functions found in eukaryotes are also present and well conserved in S. cerevisiae. In addition, it is also easily amenable to genetic manipulation. Moreover, unlike other model organisms, S. cerevisiae is concomitantly of great importance for various biotechnological applications, some of which date back to several thousands of years. S. cerevisiae's biotechnological usefulness resides in its unique biological characteristics, i.e., its fermentation capacity, accompanied by the production of alcohol and CO2 and its resilience to adverse conditions of osmolarity and low pH. Among the most prominent applications involving the use of S. cerevisiae are the ones in food, beverage -especially wine- and biofuel production industries. This review focuses exactly on the function of S. cerevisiae in these applications, alone or in conjunction with other useful microorganisms involved in these processes. Furthermore, various aspects of the potential of the reservoir of wild, environmental, S. cerevisiae isolates are examined under the perspective of their use for such applications.
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Affiliation(s)
- Maria Parapouli
- Molecular Biology Laboratory, Department of Biological applications and Technology, University of Ioannina, Ioannina, Greece
| | - Anastasios Vasileiadis
- Molecular Biology Laboratory, Department of Biological applications and Technology, University of Ioannina, Ioannina, Greece
| | - Amalia-Sofia Afendra
- Genetics Laboratory, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
| | - Efstathios Hatziloukas
- Molecular Biology Laboratory, Department of Biological applications and Technology, University of Ioannina, Ioannina, Greece
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40
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Zdaniewicz M, Satora P, Pater A, Bogacz S. Low Lactic Acid-Producing Strain of Lachancea thermotolerans as a New Starter for Beer Production. Biomolecules 2020; 10:biom10020256. [PMID: 32046171 PMCID: PMC7072388 DOI: 10.3390/biom10020256] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 11/16/2022] Open
Abstract
Growing consumer interest in new beer flavors is contributing to the application of innovative materials and non-Saccharomyces yeast in brewing. The goal of this study was to test the impact of the low lactic acid-producing Lachancea thermotolerans MN477031 strain on the process of fermenting beer wort, with two different concentrations of bitter compounds, and on the quality of the beer produced. Qualify factors were broadly analyzed, including ethanol content, apparent degree of fermentation, sugars, organic acids, free amino nitrogen, glycerol, volatile compounds, ions and so on. It was proven that the L. thermotolerans MN477031 strain demonstrated a high capacity for rapid initiation of wort fermentation, and a tolerance to hop-derived compounds. As a result, the alcohol content in beer from this method of production was approximately 20% lower, while the content of the real extract was significantly higher in comparison to commercial Safbrew T-58. This strain stands out from many strains of L. thermotolerans due to the low lactic acid production and only marginal influence on pH decrease compared to Saccharomyces cerevisiae. Therefore, the potential of MN477031 in the production of different types of beer (not only sour) is very high. The composition of volatile compounds in L. thermotolerans beer differs—not only in terms of the use of the strain, but also in hop variety.
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Almeida OGG, Pinto UM, Matos CB, Frazilio DA, Braga VF, von Zeska-Kress MR, De Martinis ECP. Does Quorum Sensing play a role in microbial shifts along spontaneous fermentation of cocoa beans? An in silico perspective. Food Res Int 2020; 131:109034. [PMID: 32247478 DOI: 10.1016/j.foodres.2020.109034] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/20/2020] [Accepted: 01/24/2020] [Indexed: 12/20/2022]
Abstract
Cocoa fermentation is a spontaneous process shaped by a variable microbial ecosystem which is assembled due to cross-feeding relationship among yeasts and bacteria, resulting in a synchronized microbial succession started by yeasts, followed by lactic acid bacteria (LAB) and finalized by acetic acid bacteria (AAB). Several studies have indicated the effect of microbial interactions in food ecosystems highlighting the importance of quorum sensing (QS) in bacterial adaptation in harsh environments modulating several phenotypes such as biofilm formation, tolerance to acid stress, bacteriocin production, competence, morphological modifications, motility, among others. However, antagonic interactions also occur, and can be marked by Quorum Quenching (QQ) activity, negatively impacting QS regulated phenotypes. Our current knowledge regarding microbial cocoa composition and functioning is based on culture-based analysis and culture-independent PCR-based methods. Therefore, we set out to investigate the application of metagenomics analysis on a classical spontaneous cocoa fermentation in order to describe: (I) the microbial taxonomic composition; (II) the functional potential of the cocoa microbiome; (III) the microbiome putative QS potential; and (IV) the microbiome QQ potential. Both aims III and IV are related to the expression of effectors that may confer advantageous traits along fermentation which can explain their dominance in specific time zones during the entire process. We have observed a bacterial succession shaped by yeasts and filamentous fungi and then Enterobacteriaceales, LAB and AAB, as well as a diverse genetic metabolic potential related to proteins and carbohydrates metabolism associated to the yeast Saccharomyces cerevisiae and members of the Enterobacteriaceales order and LAB and AAB groups. In addition, in silico evidences of interspecific QS arsenal were found in members of the genera Enterobacter, Lactobacillus, Bacillus and Pantoea, while inferences of intraspecific QS potential were found in the members of the genera Bacillus, Enterobacter, Komagataeibacter, Lactobacillus and Pantoea. In addition, a QQ potential was detected in Lactobacillus and in AAB members. These findings indicate that QS and QQ may modulate bacterial dominance in different time points during fermentation, along with cross-feeding, being responsible for their maintenance in a large time range.
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Affiliation(s)
- O G G Almeida
- Universidade de São Paulo - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Brazil
| | - U M Pinto
- Food Research Center, Universidade de São Paulo - Faculdade de Ciências Farmacêuticas, Brazil
| | - C B Matos
- Comissão Executiva do Plano da Lavoura Cacaueira- Centro de Pesquisas do Cacau (CEPLAC-CEPEC), Rod. Jorge Amado, 22 - Alto Mirante, Itabuna, BA, Brazil
| | - D A Frazilio
- Universidade de São Paulo - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Brazil
| | - V F Braga
- Universidade de São Paulo - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Brazil
| | - M R von Zeska-Kress
- Universidade de São Paulo - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Brazil
| | - E C P De Martinis
- Universidade de São Paulo - Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Brazil.
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Alperstein L, Gardner JM, Sundstrom JF, Sumby KM, Jiranek V. Yeast bioprospecting versus synthetic biology-which is better for innovative beverage fermentation? Appl Microbiol Biotechnol 2020; 104:1939-1953. [PMID: 31953561 DOI: 10.1007/s00253-020-10364-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/30/2019] [Accepted: 01/09/2020] [Indexed: 01/08/2023]
Abstract
Producers often utilise some of the many available yeast species and strains in the making of fermented alcoholic beverages in order to augment flavours, aromas, acids and textural properties. But still, the demand remains for more yeasts with novel phenotypes that not only impact sensory characteristics but also offer process and engineering advantages. Two strategies for finding such yeasts are (i) bioprospecting for novel strains and species and (ii) genetic modification of known yeasts. The latter enjoys the promise of the emerging field of synthetic biology, which, in principle, would enable scientists to create yeasts with the exact phenotype desired for a given fermentation. In this mini review, we compare and contrast advances in bioprospecting and in synthetic biology as they relate to alcoholic fermentation in brewing and wine making. We explore recent advances in fermentation-relevant recombinant technologies and synthetic biology including the Yeast 2.0 Consortium, use of environmental yeasts, challenges, constraints of law and consumer acceptance.
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Affiliation(s)
- Lucien Alperstein
- Department of Wine & Food Science, The University of Adelaide, PMB1, Glen Osmond, 5064, South Australia, Australia
| | - Jennifer M Gardner
- Department of Wine & Food Science, The University of Adelaide, PMB1, Glen Osmond, 5064, South Australia, Australia
| | - Joanna F Sundstrom
- Department of Wine & Food Science, The University of Adelaide, PMB1, Glen Osmond, 5064, South Australia, Australia.,Australian Research Council Training Centre for Innovative Wine Production, Urrbrae, South Australia, Australia
| | - Krista M Sumby
- Department of Wine & Food Science, The University of Adelaide, PMB1, Glen Osmond, 5064, South Australia, Australia.,Australian Research Council Training Centre for Innovative Wine Production, Urrbrae, South Australia, Australia
| | - Vladimir Jiranek
- Department of Wine & Food Science, The University of Adelaide, PMB1, Glen Osmond, 5064, South Australia, Australia. .,Australian Research Council Training Centre for Innovative Wine Production, Urrbrae, South Australia, Australia.
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43
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Kaplan RC, Wang Z, Usyk M, Sotres-Alvarez D, Daviglus ML, Schneiderman N, Talavera GA, Gellman MD, Thyagarajan B, Moon JY, Vázquez-Baeza Y, McDonald D, Williams-Nguyen JS, Wu MC, North KE, Shaffer J, Sollecito CC, Qi Q, Isasi CR, Wang T, Knight R, Burk RD. Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity. Genome Biol 2019; 20:219. [PMID: 31672155 PMCID: PMC6824043 DOI: 10.1186/s13059-019-1831-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 09/23/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. RESULTS Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. CONCLUSIONS Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.
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Affiliation(s)
- Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Mykhaylo Usyk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY USA
| | - Daniela Sotres-Alvarez
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA
| | - Martha L. Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago College of Medicine, Chicago, IL USA
| | | | - Gregory A. Talavera
- Division of Health Promotion and Behavioral Science, San Diego State University, San Diego, CA USA
| | - Marc D. Gellman
- Department of Psychology, University of Miami, Miami, FL USA
| | - Bharat Thyagarajan
- Division of Molecular Pathology and Genomics, University of Minnesota, Minneapolis, MN USA
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Yoshiki Vázquez-Baeza
- Jacobs School of Engineering, University of California, San Diego, La Jolla, CA USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
| | | | - Michael C. Wu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA
| | - Justin Shaffer
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
| | | | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Carmen R. Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA USA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA USA
| | - Robert D. Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461 USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY USA
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY USA
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44
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Langdon QK, Peris D, Baker EP, Opulente DA, Nguyen HV, Bond U, Gonçalves P, Sampaio JP, Libkind D, Hittinger CT. Fermentation innovation through complex hybridization of wild and domesticated yeasts. Nat Ecol Evol 2019; 3:1576-1586. [PMID: 31636426 DOI: 10.1038/s41559-019-0998-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 09/02/2019] [Indexed: 12/20/2022]
Abstract
The most common fermented beverage, lager beer, is produced by interspecies hybrids of the brewing yeast Saccharomyces cerevisiae and its wild relative S. eubayanus. Lager-brewing yeasts are not the only example of hybrid vigour or heterosis in yeasts, but the full breadth of interspecies hybrids associated with human fermentations has received less attention. Here we present a comprehensive genomic analysis of 122 Saccharomyces hybrids and introgressed strains. These strains arose from hybridization events between two to four species. Hybrids with S. cerevisiae contributions originated from three lineages of domesticated S. cerevisiae, including the major wine-making lineage and two distinct brewing lineages. In contrast, the undomesticated parents of these interspecies hybrids were all from wild Holarctic or European lineages. Most hybrids have inherited a mitochondrial genome from a parent other than S. cerevisiae, which recent functional studies suggest could confer adaptation to colder temperatures. A subset of hybrids associated with crisp flavour profiles, including both lineages of lager-brewing yeasts, have inherited inactivated S. cerevisiae alleles of critical phenolic off-flavour genes and/or lost functional copies from the wild parent through multiple genetic mechanisms. These complex hybrids shed light on the convergent and divergent evolutionary trajectories of interspecies hybrids and their impact on innovation in lager brewing and other diverse fermentation industries.
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Affiliation(s)
- Quinn K Langdon
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
| | - David Peris
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Food Biotechnology, Institute of Agrochemistry and Food Technology, CSIC, Valencia, Spain
| | - EmilyClare P Baker
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Dana A Opulente
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Huu-Vang Nguyen
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ursula Bond
- Department of Microbiology, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Paula Gonçalves
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática de Levaduras, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA. .,DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA. .,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
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45
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Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: major ecological adaptations and evolutionary transitions. Biol Rev Camb Philos Soc 2019; 94:1443-1476. [PMID: 31021528 PMCID: PMC6850671 DOI: 10.1111/brv.12510] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/10/2019] [Accepted: 03/13/2019] [Indexed: 12/13/2022]
Abstract
Fungi are a highly diverse group of heterotrophic eukaryotes characterized by the absence of phagotrophy and the presence of a chitinous cell wall. While unicellular fungi are far from rare, part of the evolutionary success of the group resides in their ability to grow indefinitely as a cylindrical multinucleated cell (hypha). Armed with these morphological traits and with an extremely high metabolical diversity, fungi have conquered numerous ecological niches and have shaped a whole world of interactions with other living organisms. Herein we survey the main evolutionary and ecological processes that have guided fungal diversity. We will first review the ecology and evolution of the zoosporic lineages and the process of terrestrialization, as one of the major evolutionary transitions in this kingdom. Several plausible scenarios have been proposed for fungal terrestralization and we here propose a new scenario, which considers icy environments as a transitory niche between water and emerged land. We then focus on exploring the main ecological relationships of Fungi with other organisms (other fungi, protozoans, animals and plants), as well as the origin of adaptations to certain specialized ecological niches within the group (lichens, black fungi and yeasts). Throughout this review we use an evolutionary and comparative-genomics perspective to understand fungal ecological diversity. Finally, we highlight the importance of genome-enabled inferences to envision plausible narratives and scenarios for important transitions.
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Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Department of Genomics and Bioinformatics, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF)08003BarcelonaSpain
- ICREA, Pg. Lluís Companys 2308010BarcelonaSpain
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46
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Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology. mBio 2019; 10:mBio.00388-19. [PMID: 31040238 PMCID: PMC6495373 DOI: 10.1128/mbio.00388-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms—yeast in this case—from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio- and experimental archaeology that aim to reconstruct ancient artifacts and products. Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research.
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Shwaiki LN, Arendt EK, Lynch KM, Thery TLC. Inhibitory effect of four novel synthetic peptides on food spoilage yeasts. Int J Food Microbiol 2019; 300:43-52. [PMID: 31035250 DOI: 10.1016/j.ijfoodmicro.2019.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 04/08/2019] [Accepted: 04/10/2019] [Indexed: 12/31/2022]
Abstract
The spoilage of foods caused by the growth of undesirable yeast species is a problem in the food industry. Yeast species such as Zygosaccharomyces bailii, Zygosaccharomyces rouxii, Debaryomyces hansenii, Kluyveromyces lactis and Saccharomyces cerevisiae have been encountered in foods such as high sugar products, fruit juices, wine, mayonnaise, chocolate and soft drinks. The demand for new methods of preservations has increased because of the negative association attached to chemical preservatives. The sequence of a novel short peptide (KKFFRAWWAPRFLK-NH2) was modified to generate three versions of this original peptide. These peptides were tested for the inhibition of the yeasts mentioned above, allowing for the better understanding of their residue modifications. The range of the minimum inhibitory concentration was between 25 and 200 μg/mL. Zygosaccharomyces bailii was the most sensitive strain to the peptides, while Zygosaccharomyces rouxii was the most resistant. Membrane permeabilisation was found to be responsible for yeast inhibition at a level which was a two-fold increase of the MIC (400 μg/mL). The possibility of the production of reactive oxygen species was also assessed but was not recognised as a factor involved for the peptides' mode of action. Their stability in different environments was also tested, focusing on high salt, pH and thermal stability. The newly designed peptides showed good antifungal activity against some common food spoilage yeasts and has been proven effective in the application in Fanta Orange. These efficient novel peptides represent a new source of food preservation that can be used as an alternative for current controversial preservatives used in the food industry.
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Affiliation(s)
- Laila N Shwaiki
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Elke K Arendt
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland; APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | - Kieran M Lynch
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
| | - Thibaut L C Thery
- School of Food and Nutritional Sciences, University College Cork, Cork, Ireland
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48
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Brouwers N, Gorter de Vries AR, van den Broek M, Weening SM, Elink Schuurman TD, Kuijpers NGA, Pronk JT, Daran JMG. In vivo recombination of Saccharomyces eubayanus maltose-transporter genes yields a chimeric transporter that enables maltotriose fermentation. PLoS Genet 2019; 15:e1007853. [PMID: 30946741 PMCID: PMC6448828 DOI: 10.1371/journal.pgen.1007853] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/26/2018] [Indexed: 11/18/2022] Open
Abstract
Saccharomyces eubayanus is the non-S. cerevisiae parent of the lager-brewing hybrid S. pastorianus. In contrast to most S. cerevisiae and Frohberg-type S. pastorianus strains, S. eubayanus cannot utilize the α-tri-glucoside maltotriose, a major carbohydrate in brewer’s wort. In Saccharomyces yeasts, utilization of maltotriose is encoded by the subtelomeric MAL gene family, and requires transporters for maltotriose uptake. While S. eubayanus strain CBS 12357T harbors four SeMALT genes which enable uptake of the α-di-glucoside maltose, it lacks maltotriose transporter genes. In S. cerevisiae, sequence identity indicates that maltotriose and maltose transporters likely evolved from a shared ancestral gene. To study the evolvability of maltotriose utilization in S. eubayanus CBS 12357T, maltotriose-assimilating mutants obtained after UV mutagenesis were subjected to laboratory evolution in carbon-limited chemostat cultures on maltotriose-enriched wort. An evolved strain showed improved maltose and maltotriose fermentation in 7 L fermenter experiments on industrial wort. Whole-genome sequencing revealed a novel mosaic SeMALT413 gene, resulting from repeated gene introgressions by non-reciprocal translocation of at least three SeMALT genes. The predicted tertiary structure of SeMalT413 was comparable to the original SeMalT transporters, but overexpression of SeMALT413 sufficed to enable growth on maltotriose, indicating gene neofunctionalization had occurred. The mosaic structure of SeMALT413 resembles the structure of S. pastorianus maltotriose-transporter gene SpMTY1, which has high sequences identity to alternatingly S. cerevisiae MALx1, S. paradoxus MALx1 and S. eubayanus SeMALT3. Evolution of the maltotriose transporter landscape in hybrid S. pastorianus lager-brewing strains is therefore likely to have involved mechanisms similar to those observed in the present study. Fermentation of the wort sugar maltotriose is critical for the flavor profile obtained during beer brewing. The recently discovered yeast Saccharomyces eubayanus is gaining popularity as an alternative to S. pastorianus and S. cerevisiae for brewing, however it is unable to utilize maltotriose. Here, a combination of non-GMO mutagenesis and laboratory evolution of the S. eubayanus type strain CBS 12357T was used to enable maltotriose fermentation and improve brewing performance. The improved strain expressed a novel transporter gene, SeMALT413, which was formed by recombination between three different SeMALT maltose-transporter genes. Overexpression of SeMALT413 in CBS 12357T confirmed its neofunctionalization as a maltotriose transporter. As the S. pastorianus maltotriose transporter SpMty1 has a mosaic structure similar to SeMalT413, maltotriose utilization likely involved similar recombination events during the domestication of current lager brewing strains. Based on a posteriori sequence analysis, the emergence of gene functions has been attributed to gene neofunctionalization in a broad range of organisms. The real-time observation of neofunctionalization during laboratory evolution constitutes an important validation of the relevance and importance of this mechanism for Darwinian evolution.
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Affiliation(s)
- Nick Brouwers
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Arthur R. Gorter de Vries
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Susan M. Weening
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | | | - Niels G. A. Kuijpers
- HEINEKEN Supply Chain B.V., Global Innovation and Research, Zoeterwoude, Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Jean-Marc G. Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
- * E-mail:
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49
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Baker EP, Hittinger CT. Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function. PLoS Genet 2019; 15:e1007786. [PMID: 30946740 PMCID: PMC6448821 DOI: 10.1371/journal.pgen.1007786] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/25/2018] [Indexed: 11/23/2022] Open
Abstract
At the molecular level, the evolution of new traits can be broadly divided between changes in gene expression and changes in protein-coding sequence. For proteins, the evolution of novel functions is generally thought to proceed through sequential point mutations or recombination of whole functional units. In Saccharomyces, the uptake of the sugar maltotriose into the cell is the primary limiting factor in its utilization, but maltotriose transporters are relatively rare, except in brewing strains. No known wild strains of Saccharomyces eubayanus, the cold-tolerant parent of hybrid lager-brewing yeasts (Saccharomyces cerevisiae x S. eubayanus), are able to consume maltotriose, which limits their ability to fully ferment malt extract. In one strain of S. eubayanus, we found a gene closely related to a known maltotriose transporter and were able to confer maltotriose consumption by overexpressing this gene or by passaging the strain on maltose. Even so, most wild strains of S. eubayanus lack native maltotriose transporters. To determine how this rare trait could evolve in naive genetic backgrounds, we performed an adaptive evolution experiment for maltotriose consumption, which yielded a single strain of S. eubayanus able to grow on maltotriose. We mapped the causative locus to a gene encoding a novel chimeric transporter that was formed by an ectopic recombination event between two genes encoding transporters that are unable to import maltotriose. In contrast to classic models of the evolution of novel protein functions, the recombination breakpoints occurred within a single functional domain. Thus, the ability of the new protein to carry maltotriose was likely acquired through epistatic interactions between independently evolved substitutions. By acquiring multiple mutations at once, the transporter rapidly gained a novel function, while bypassing potentially deleterious intermediate steps. This study provides an illuminating example of how recombination between paralogs can establish novel interactions among substitutions to create adaptive functions. Hybrids of the yeasts Saccharomyces cerevisiae and Saccharomyces eubayanus (lager-brewing yeasts) dominate the modern brewing industry. S. cerevisiae, also known as baker’s yeast, is well-known for its role in industry and scientific research. Less well recognized is S. eubayanus, which was only discovered as a pure species in 2011. While most lager-brewing yeasts rapidly and completely utilize the important brewing sugar maltotriose, no strain of S. eubayanus isolated to date is known to do so. Despite being unable to consume maltotriose, we identified one strain of S. eubayanus carrying a gene for a functional maltotriose transporter, although most strains lack this gene. During an adaptive evolution experiment, a strain of S. eubayanus without native maltotriose transporters evolved the ability to grow on maltotriose. Maltotriose consumption in the evolved strain resulted from a chimeric transporter that arose by shuffling genes encoding parent proteins that were unable to transport maltotriose. Traditionally, functional chimeric proteins are thought to evolve by shuffling discrete functional domains or modules, but the breakpoints in the chimera studied here occurred within the single functional module of the protein. These results support the less well-recognized role of shuffling duplicate gene sequences to generate novel proteins with adaptive functions.
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Affiliation(s)
- EmilyClare P. Baker
- Laboratory of Genetics, Microbiology Doctoral Training Program, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Chris Todd Hittinger
- Laboratory of Genetics, Microbiology Doctoral Training Program, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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50
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Sessou P, Keisam S, Tuikhar N, Gagara M, Farougou S, Jeyaram K. High-Throughput Illumina MiSeq Amplicon Sequencing of Yeast Communities Associated With Indigenous Dairy Products From Republics of Benin and Niger. Front Microbiol 2019; 10:594. [PMID: 31001212 PMCID: PMC6456676 DOI: 10.3389/fmicb.2019.00594] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/08/2019] [Indexed: 12/19/2022] Open
Abstract
Traditional Wagashi cheese and fermented cow milk are among the most popular dairy products appreciated by people from Benin, Niger, and the neighboring region. These products are the main source of protein in the diet of the low-income population in the region. The fermented milk is prepared by spontaneous fermentation without back-slopping. Whereas, the leaf extract of Calotropis procera is used for curdling the milk to prepare the soft Wagashi cheese. The present study aims to provide in-depth analysis of yeast communities associated with these traditional milk products by high-throughput Illumina MiSeq amplicon sequencing of internal transcribed spacer (ITS) region of fungal rRNA genes. A total of 60 samples, 20 samples of fermented milk each from Benin and Niger, and 20 samples of Wagashi cheese from Benin were used for analysis. The metagenomic investigation revealed that Kluyveromyces marxianus, Saccharomyces cerevisiae, Candida parapsilosis, and Sagenomella keratitidis were the predominant yeast species present in the traditional milk products. Furthermore, we noticed a high presence of K. marxianus (61.1% relative abundance) in the Wagashi cheese and S. cerevisiae (28.4% relative abundance) in the fermented milk of Niger. The presence of potential pathogenic yeast C. parapsilosis and S. keratitidis in these African milk products calls for further investigation to assess their safety. The predominant yeast K. marxianus and S. cerevisiae, recognized with generally regarded as safe (GRAS) status, could be further selected as starter culture along with lactic acid bacteria for developing controlled fermentation processes with enhanced product quality and safety.
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Affiliation(s)
- Philippe Sessou
- Research Unit on Communicable Diseases, Laboratory of Research in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Santosh Keisam
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, India
| | - Ngangyola Tuikhar
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, India
| | | | - Souaïbou Farougou
- Research Unit on Communicable Diseases, Laboratory of Research in Applied Biology, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Kumaraswamy Jeyaram
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, India
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