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Zheng A, Wei C, Liu J, Bu N, Liu D. Deciphering the Mechanism by Which Carbon Dioxide Extends the Shelf Life of Raw Milk: A Microbiomics- and Metabolomics-Based Approach. Molecules 2024; 29:329. [PMID: 38257241 PMCID: PMC10819274 DOI: 10.3390/molecules29020329] [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: 12/01/2023] [Revised: 12/26/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Microbial community succession in raw milk determines its quality and storage period. In this study, carbon dioxide (CO2) at 2000 ppm was used to treat raw milk to investigate the mechanism of extending the shelf life of raw milk by CO2 treatment from the viewpoint of microbial colonies and metabolites. The results showed that the shelf life of CO2-treated raw milk was extended to 16 days at 4 °C, while that of the control raw milk was only 6 days. Microbiomics analysis identified 221 amplicon sequence variants (ASVs) in raw milk, and the alpha diversity of microbial communities increased (p < 0.05) with the extension of storage time. Among them, Pseudomonas, Actinobacteria and Serratia were the major microbial genera responsible for the deterioration of raw milk, with a percentage of 85.7%. A combined metagenomics and metabolomics analysis revealed that microorganisms altered the levels of metabolites, such as pyruvic acid, glutamic acid, 5'-cmp, arginine, 2-propenoic acid and phenylalanine, in the raw milk through metabolic activities, such as ABC transporters, pyrimidine metabolism, arginine and proline metabolism and phenylalanine metabolism, and reduced the shelf life of raw milk. CO2 treatment prolonged the shelf life of raw milk by inhibiting the growth of Gram-negative aerobic bacteria, such as Acinetobacter guillouiae, Pseudomonas fluorescens, Serratia liquefaciens and Pseudomonas simiae.
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Affiliation(s)
- Anran Zheng
- School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (A.Z.)
- School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Chaokun Wei
- School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (A.Z.)
- School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Jun Liu
- School of Life Sciences, Hubei Normmal University, Huangshi 435002, China;
| | - Ningxia Bu
- School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (A.Z.)
- School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
| | - Dunhua Liu
- School of Animal Science and Technology, Ningxia University, Yinchuan 750021, China; (A.Z.)
- School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
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2
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Luo X, Li Y, Zhong K, Luo D, Wu Y, Gao H. Discovering the effect of co-fermentation involving Saccharomyces cerevisiae and Schizosaccharomyces pombe on the sensory quality improvement of mandarin wine based on metabolites and transcriptomic profiles. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:7932-7940. [PMID: 37499161 DOI: 10.1002/jsfa.12885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 07/02/2023] [Accepted: 07/28/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND Mandarin wine has high added value, which can extend the industry chain of mandarins with excellent economic results. However, innovative fermentation methods are urgently needed to improve the typical taste and flavor characteristics of mandarin wine. In this study, the effect and underlying mechanism of co-fermentation with Saccharomyces cerevisiae and Schizosaccharomyces pombe on the characteristics of mandarin wine were investigated based on integrated metabolomic and transcriptomic analyses. RESULTS In comparison with fermentation with only S. cerevisiae, the mandarin wine produced from co-fermentation with S. cerevisiae and Sc. pombe had a higher pH value, lower malic acid content, and more abundant free amino acids, resulting in better sensory evaluation scores. The introduction of Sc. pombe extended the stage of alcoholic fermentation and enhanced the richness and diversity of volatile compounds, especially floral and fruity aroma compounds, including ethyl hexanoate, ethyl caprylate, ethyl enanthate, 1-heptanol, and phenylethyl alcohol. he significantly differential metabolites and varying genes were mainly found in pathways of glycolysis, pyruvate metabolism, the citrate cycle, and amino acid metabolism. CONCLUSION Co-fermentation with S. cerevisiae and Sc. pombe showed advantages in producing distinctive taste and flavor of mandarin wine in comparison with fermentation with only S. cerevisiae. This study can inspire new co-fermentation strategies to improve the sensory quality of mandarin wine. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xiaoqin Luo
- College of Biomass Science and Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, China
| | - Yumeng Li
- College of Biomass Science and Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, China
| | - Kai Zhong
- College of Biomass Science and Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, China
| | - Dong Luo
- Sichuan MingFuBang Agricultural Science and Technology Co., LTD, Meishan, China
| | - Yanping Wu
- College of Biomass Science and Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, China
| | - Hong Gao
- College of Biomass Science and Engineering and Healthy Food Evaluation Research Center, Sichuan University, Chengdu, China
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3
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Bordet F, Romanet R, Bahut F, Ballester J, Eicher C, Peña C, Ferreira V, Gougeon R, Julien-Ortiz A, Roullier-Gall C, Alexandre H. Expanding the diversity of Chardonnay aroma through the metabolic interactions of Saccharomyces cerevisiae cocultures. Front Microbiol 2023; 13:1032842. [PMID: 36845971 PMCID: PMC9947296 DOI: 10.3389/fmicb.2022.1032842] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/02/2022] [Indexed: 02/11/2023] Open
Abstract
Yeast co-inoculations in winemaking are often studied in the framework of modulating the aromatic profiles of wines. Our study aimed to investigate the impact of three cocultures and corresponding pure cultures of Saccharomyces cerevisiae on the chemical composition and the sensory profile of Chardonnay wine. Coculture makes it possible to obtain completely new aromatic expressions that do not exist in the original pure cultures attributed to yeast interactions. Esters, fatty acids and phenol families were identified as affected. The sensory profiles and metabolome of the cocultures, corresponding pure cultures and associated wine blends from both pure cultures were found to be different. The coculture did not turn out to be the addition of the two pure culture wines, indicating the impact of interaction. High resolution mass spectrometry revealed thousands of cocultures biomarkers. The metabolic pathways involved in these wine composition changes were highlighted, most of them belonging to nitrogen metabolism.
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Affiliation(s)
- Fanny Bordet
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France,Lallemand SAS, Blagnac, France,*Correspondence: Fanny Bordet,
| | - Rémy Romanet
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France
| | - Florian Bahut
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France,Lallemand SAS, Blagnac, France
| | - Jordi Ballester
- Centre des Sciences du Goût et de l’Alimentation, CNRS, INRAE, Institut Agro, Université Bourgogne Franche-Comté, Dijon, France
| | - Camille Eicher
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France
| | - Cristina Peña
- Dpt. Química Analítica, Facultad de Ciencias, University of Zaragoza, Zaragoza, Spain
| | - Vicente Ferreira
- Dpt. Química Analítica, Facultad de Ciencias, University of Zaragoza, Zaragoza, Spain
| | - Régis Gougeon
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France,DIVVA (Développement Innovation Vigne Vin Aliments) Platform/PAM UMR, IUVV, Dijon, France
| | | | - Chloé Roullier-Gall
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France
| | - Hervé Alexandre
- PAM UMR A 02.102, Univ. Bourgogne Franche-Comté, Institut Agro Dijon, IUVV, Dijon, France
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A Transcriptomic Analysis of Higher-Order Ecological Interactions in a Eukaryotic Model Microbial Ecosystem. mSphere 2022; 7:e0043622. [PMID: 36259715 PMCID: PMC9769528 DOI: 10.1128/msphere.00436-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Nonlinear ecological interactions within microbial ecosystems and their contribution to ecosystem functioning remain largely unexplored. Higher-order interactions, or interactions in systems comprised of more than two members that cannot be explained by cumulative pairwise interactions, are particularly understudied, especially in eukaryotic microorganisms. The wine fermentation ecosystem presents an ideal model to study yeast ecosystem establishment and functioning. Some pairwise ecological interactions between wine yeast species have been characterized, but very little is known about how more complex, multispecies systems function. Here, we evaluated nonlinear ecosystem properties by determining the transcriptomic response of Saccharomyces cerevisiae to pairwise versus tri-species culture. The transcriptome revealed that genes expressed during pairwise coculture were enriched in the tri-species data set but also that just under half of the data set comprised unique genes attributed to a higher-order response. Through interactive protein-association network visualizations, a holistic cell-wide view of the gene expression data was generated, which highlighted known stress response and metabolic adaptation mechanisms which were specifically activated during tri-species growth. Further, extracellular metabolite data corroborated that the observed differences were a result of a biotic stress response. This provides exciting new evidence showing the presence of higher-order interactions within a model microbial ecosystem. IMPORTANCE Higher-order interactions are one of the major blind spots in our understanding of microbial ecosystems. These systems remain largely unpredictable and are characterized by nonlinear dynamics, in particular when the system is comprised of more than two entities. By evaluating the transcriptomic response of S. cerevisiae to an increase in culture complexity from a single species to two- and three-species systems, we were able to confirm the presence of a unique response in the more complex setting that could not be explained by the responses observed at the pairwise level. This is the first data set that provides molecular targets for further analysis to explain unpredictable ecosystem dynamics in yeast.
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A Proteomic Landscape of Candida albicans in the Stepwise Evolution to Fluconazole Resistance. Antimicrob Agents Chemother 2022; 66:e0210521. [PMID: 35343782 DOI: 10.1128/aac.02105-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
As an opportunistic fungal pathogen, Candida albicans is a major cause of superficial and systemic infections in immunocompromised patients. The increasing rate of azole resistance in C. albicans has brought further challenges to clinical therapy. In this study, we collected five isogenic C. albicans strains recovered over discrete intervals from an HIV-infected patient who suffered 2-year recurrent oropharyngeal candidiasis. Azole resistance was known from the clinical history to have developed gradually in this patient, and this was confirmed by MIC assays of each strain. Proteomic techniques can be used to investigate more comprehensively how resistance develops in pathogenic fungi over time. Our study is the first to use tandem mass tag (TMT) labeling combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology to investigate the acquired resistance mechanisms of serial C. albicans isolates at the proteomic level. A total of 4,029 proteins have been identified, of which 3,766 have been quantified. Compared with Ca1, bioinformatics analysis showed that differentially expressed proteins were mainly associated with aspects such as the downregulation of glycolysis/gluconeogenesis, pyruvate metabolism, fatty acid degradation, and oxidative stress response proteins in all four subsequent strains but, remarkably, the activation of amino acid metabolism in Ca8 and Ca14 and increased protection against osmotic stress or excessive copper toxicity, upregulation of respiratory chain activity, and suppression of iron transport in Ca17. By tracing proteomic alterations in this set of isogenic resistance isolates, we acquire mechanistic insight into the steps involved in the acquisition of azole resistance in C. albicans.
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Gianvito PD, Englezos V, Rantsiou K, Cocolin L. Bioprotection strategies in winemaking. Int J Food Microbiol 2022; 364:109532. [PMID: 35033974 DOI: 10.1016/j.ijfoodmicro.2022.109532] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 01/30/2023]
Abstract
Worldwide the interest for biological control of food spoilage microorganisms has significantly increased over the last decade. Wine makes no exception to this trend, as consumer demands for wines free of preservatives that are considered negative for human health, increase. Biological control during wine fermentation aims at producing high quality wines, while minimizing, or even eliminating, the use of chemical additives. Its success lies in the inoculation of microorganisms to prevent, inhibit or kill undesired microbes, therefore maintaining wine spoilage at the lowest level. The food industry already makes use of this practice, with dedicated commercial microbes already on the market. In winemaking, there are commercial microbes currently under investigation, particularly with the aim to reduce or replace the use of sulphur dioxide. In this review, the potential of wine yeasts and lactic acid bacteria as bioprotection agents and their mechanisms of action during wine fermentation are presented.
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Affiliation(s)
- Paola Di Gianvito
- Università degli Studi di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Largo Braccini 2, 10095 Grugliasco, Italy
| | - Vasileios Englezos
- Università degli Studi di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Largo Braccini 2, 10095 Grugliasco, Italy
| | - Kalliopi Rantsiou
- Università degli Studi di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Largo Braccini 2, 10095 Grugliasco, Italy
| | - Luca Cocolin
- Università degli Studi di Torino, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Largo Braccini 2, 10095 Grugliasco, Italy.
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Vicente J, Navascués E, Calderón F, Santos A, Marquina D, Benito S. An Integrative View of the Role of Lachancea thermotolerans in Wine Technology. Foods 2021; 10:foods10112878. [PMID: 34829158 PMCID: PMC8625220 DOI: 10.3390/foods10112878] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 11/23/2022] Open
Abstract
The interest in Lachancea thermotolerans, a yeast species with unusual characteristics, has notably increased in all ecological, evolutionary, and industrial aspects. One of the key characteristics of L. thermotolerans is the production of high quantities of lactic acid compared to other yeast species. Its evolution has mainly been driven by the influence of the environment and domestication, allowing several metabolic traits to arise. The molecular regulation of the fermentative process in L. thermotolerans shows interesting routes that play a complementary or protective role against fermentative stresses. One route that is activated under this condition is involved in the production of lactic acid, presenting a complete system for its production, showing the involvement of several enzymes and transporters. In winemaking, the use of L. thermotolerans is nowadays mostly focused in early–medium-maturity grape varieties, in which over-ripening can produce wines lacking acidity and with high concentrations of ethanol. Recent studies have reported new positive influences on quality apart from lactic acid acidification, such as improvements in color, glutathione production, aroma, malic acid, polysaccharides, or specific enzymatic activities that constitute interesting new criteria for selecting better strains. This positive influence on winemaking has increased the availability of commercial strains during recent years, allowing comparisons among some of those products. Initially, the management of L. thermotolerans was thought to be combined with Saccaharomyces cerevisiae to properly end alcoholic fermentation, but new studies are innovating and reporting combinations with other key enological microorganisms such as Schizosaccharomyces pombe, Oenocous oeni, Lactiplantibacillus plantarum, or other non-Saccharomyces.
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Affiliation(s)
- Javier Vicente
- Unit of Microbiology, Genetics, Physiology and Microbiology Department, Biology Faculty, Complutense University of Madrid, Ciudad Universitaria, S/N, 28040 Madrid, Spain; (J.V.); (A.S.); (D.M.)
| | - Eva Navascués
- Department of Chemistry and Food Technology, Polytechnic University of Madrid, Ciudad Universitaria, S/N, 28040 Madrid, Spain; (E.N.); (F.C.)
- Pago de Carraovejas, Camino de Carraovejas, S/N, 47300 Valladolid, Spain
| | - Fernando Calderón
- Department of Chemistry and Food Technology, Polytechnic University of Madrid, Ciudad Universitaria, S/N, 28040 Madrid, Spain; (E.N.); (F.C.)
| | - Antonio Santos
- Unit of Microbiology, Genetics, Physiology and Microbiology Department, Biology Faculty, Complutense University of Madrid, Ciudad Universitaria, S/N, 28040 Madrid, Spain; (J.V.); (A.S.); (D.M.)
| | - Domingo Marquina
- Unit of Microbiology, Genetics, Physiology and Microbiology Department, Biology Faculty, Complutense University of Madrid, Ciudad Universitaria, S/N, 28040 Madrid, Spain; (J.V.); (A.S.); (D.M.)
| | - Santiago Benito
- Department of Chemistry and Food Technology, Polytechnic University of Madrid, Ciudad Universitaria, S/N, 28040 Madrid, Spain; (E.N.); (F.C.)
- Correspondence: ; Tel.: +34-9133-63710 or +34-9133-63984
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8
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Reed CJ, Hutinet G, de Crécy-Lagard V. Comparative Genomic Analysis of the DUF34 Protein Family Suggests Role as a Metal Ion Chaperone or Insertase. Biomolecules 2021; 11:1282. [PMID: 34572495 PMCID: PMC8469502 DOI: 10.3390/biom11091282] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022] Open
Abstract
Members of the DUF34 (domain of unknown function 34) family, also known as the NIF3 protein superfamily, are ubiquitous across superkingdoms. Proteins of this family have been widely annotated as "GTP cyclohydrolase I type 2" through electronic propagation based on one study. Here, the annotation status of this protein family was examined through a comprehensive literature review and integrative bioinformatic analyses that revealed varied pleiotropic associations and phenotypes. This analysis combined with functional complementation studies strongly challenges the current annotation and suggests that DUF34 family members may serve as metal ion insertases, chaperones, or metallocofactor maturases. This general molecular function could explain how DUF34 subgroups participate in highly diversified pathways such as cell differentiation, metal ion homeostasis, pathogen virulence, redox, and universal stress responses.
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Affiliation(s)
- Colbie J. Reed
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (C.J.R.); (G.H.)
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (C.J.R.); (G.H.)
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (C.J.R.); (G.H.)
- Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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9
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Zilelidou EA, Nisiotou A. Understanding Wine through Yeast Interactions. Microorganisms 2021; 9:microorganisms9081620. [PMID: 34442699 PMCID: PMC8399628 DOI: 10.3390/microorganisms9081620] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Wine is a product of microbial activities and microbe–microbe interactions. Yeasts are the principal microorganisms responsible for the evolution and fulfillment of alcoholic fermentation. Several species and strains coexist and interact with their environment and with each other during the fermentation course. Yeast–yeast interactions occur even from the early stages of fermentation, determining yeast community structure and dynamics during the process. Different types of microbial interactions (e.g., mutualism and commensalism or competition and amensalism) may exert positive or negative effects, respectively, on yeast populations. Interactions are intimately linked to yeast metabolic activities that influence the wine analytical profile and shape the wine character. In this context, much attention has been given during the last years to the interactions between Saccharomyces cerevisiae (SC) and non-Saccharomyces (NS) yeast species with respect to their metabolic contribution to wine quality. Yet, there is still a significant lack of knowledge on the interaction mechanisms modulating yeast behavior during mixed culture fermentation, while much less is known about the interactions between the various NS species or between SC and Saccharomyces non-cerevisiae (SNC) yeasts. There is still much to learn about their metabolic footprints and the genetic mechanisms that alter yeast community equilibrium in favor of one species or another. Gaining deeper insights on yeast interactions in the grape–wine ecosystem sets the grounds for understanding the rules underlying the function of the wine microbial system and provides means to better control and improve oenological practices.
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10
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Proteomic analysis of serial isolates of Trichosporon asahii identifies host-specific adaptations using the TMT/MRM approach. J Proteomics 2021; 245:104309. [PMID: 34153541 DOI: 10.1016/j.jprot.2021.104309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/03/2021] [Accepted: 06/11/2021] [Indexed: 11/23/2022]
Abstract
The opportunistic fungal pathogen Trichosporon asahii (T. asahii) is an important causal agent of mortality in immunocompromised patients and associated with frequent relapses, even with sufficient antifungal treatment. Investigating the proteomes of initial and recurrent isolates may help to identify within-host adaptive changes. In this study, using tandem mass tag (TMT)-labeling combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) technology, we analyzed the proteomes of two T. asahii strains that were isolated 15 years apart from the same patient who suffered initial and recurrent episodes of systemic disseminated trichosporonosis. A total of 597 differentially expressed proteins were identified. Functional analysis showed that the increased proteins were primarily concentrated on peptide/protein/energy/drug metabolism and translation. Most of the results were determined to be consistent with the findings of phenotypic assays, such as tests for drug susceptibility, temperature growth, biofilm formation, melanization and paromomycin assays. Moreover, we performed multiple reaction monitoring (MRM) mass spectrometry to verify 27 candidate proteins, and the results of this experiment were also highly consistent with the results of the TMT analysis. Therefore, to the best of our knowledge, these data provide the first molecular evidence of how the T. asahii proteome changes related to host-specific adaptation during human infection. SIGNIFICANCE: Systemic infection with Trichosporon asahii (T. asahii) has recently been recognized as an important causal agent of mortality in immunocompromised patients. Although triazole treatment usually works efficiently in the early phase of infection, many patients relapse. Hence, comparative analyses of the proteomics of initial and recurrent isolates may reveal evidence of adaptive changes within the host. Our study demonstrates that the recurrent strain has undergone proteomic changes using tandem mass tag (TMT)-labeling combined with liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Moreover, the results of phenotypic assays, including drug susceptibility, temperature growth, biofilm formation, melanization and paromomycin assays, were highly consistent with the proteomic changes, and multiple reaction monitoring (MRM) verification also showed similar trends to the TMT results. In summary, our study is the first to investigate the adaptation of T. asahii under pressure from antifungal chemotherapy and host immune responses.
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Conacher CG, Luyt NA, Naidoo-Blassoples RK, Rossouw D, Setati ME, Bauer FF. The ecology of wine fermentation: a model for the study of complex microbial ecosystems. Appl Microbiol Biotechnol 2021; 105:3027-3043. [PMID: 33834254 DOI: 10.1007/s00253-021-11270-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/30/2021] [Accepted: 04/04/2021] [Indexed: 12/11/2022]
Abstract
The general interest in microbial ecology has skyrocketed over the past decade, driven by technical advances and by the rapidly increasing appreciation of the fundamental services that these ecosystems provide. In biotechnology, ecosystems have many more functionalities than single species, and, if properly understood and harnessed, will be able to deliver better outcomes for almost all imaginable applications. However, the complexity of microbial ecosystems and of the interactions between species has limited their applicability. In research, next generation sequencing allows accurate mapping of the microbiomes that characterise ecosystems of biotechnological and/or medical relevance. But the gap between mapping and understanding, to be filled by "functional microbiomics", requires the collection and integration of many different layers of complex data sets, from molecular multi-omics to spatial imaging technologies to online ecosystem monitoring tools. Holistically, studying the complexity of most microbial ecosystems, consisting of hundreds of species in specific spatial arrangements, is beyond our current technical capabilities, and simpler model systems with fewer species and reduced spatial complexity are required to establish the fundamental rules of ecosystem functioning. One such ecosystem, the ecosystem responsible for natural alcoholic fermentation, can provide an excellent tool to study evolutionarily relevant interactions between multiple species within a relatively easily controlled environment. This review will critically evaluate the approaches that are currently implemented to dissect the cellular and molecular networks that govern this ecosystem. KEY POINTS: • Evolutionarily isolated fermentation ecosystem can be used as an ecological model. • Experimental toolbox is gearing towards mechanistic understanding of this ecosystem. • Integration of multidisciplinary datasets is key to predictive understanding.
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Affiliation(s)
- C G Conacher
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - N A Luyt
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - R K Naidoo-Blassoples
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - D Rossouw
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - M E Setati
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa
| | - F F Bauer
- Department of Viticulture and Oenology, South African Grape and Wine Research Institute, Stellenbosch University, Private Bag X1, Stellenbosch, 7600, South Africa.
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12
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Conacher CG, Rossouw D, Bauer FFB. Peer pressure: evolutionary responses to biotic pressures in wine yeasts. FEMS Yeast Res 2020; 19:5593956. [PMID: 31626300 DOI: 10.1093/femsyr/foz072] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/16/2019] [Indexed: 12/19/2022] Open
Abstract
In the macroscopic world, ecological interactions between multiple species of fauna and flora are recognised as major role-players in the evolution of any particular species. By comparison, research on ecological interactions as a driver of evolutionary adaptation in microbial ecosystems has been neglected. The evolutionary history of the budding yeast Saccharomyces cerevisiae has been extensively researched, providing an unmatched foundation for exploring adaptive evolution of microorganisms. However, in most studies, the habitat is only defined by physical and chemical parameters, and little attention is paid to the impact of cohabiting species. Such ecological interactions arguably provide a more relevant evolutionary framework. Within the genomic phylogenetic tree of S. cerevisiae strains, wine associated isolates form a distinct clade, also matched by phenotypic evidence. This domestication signature in genomes and phenomes suggests that the wine fermentation environment is of significant evolutionary relevance. Data also show that the microbiological composition of wine fermentation ecosystems is dominated by the same species globally, suggesting that these species have co-evolved within this ecosystem. This system therefore presents an excellent model for investigating the origins and mechanisms of interspecific yeast interactions. This review explores the role of biotic stress in the adaptive evolution of wine yeast.
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Affiliation(s)
- C G Conacher
- Institute for Wine Biotechnology, Department of Oenology and Viticulture, Private Bag X1, Stellenbosch University, Stellenbosch 7600, South Africa
| | - D Rossouw
- Institute for Wine Biotechnology, Department of Oenology and Viticulture, Private Bag X1, Stellenbosch University, Stellenbosch 7600, South Africa
| | - F F B Bauer
- Institute for Wine Biotechnology, Department of Oenology and Viticulture, Private Bag X1, Stellenbosch University, Stellenbosch 7600, South Africa
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13
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Real-time monitoring of population dynamics and physical interactions in a synthetic yeast ecosystem by use of multicolour flow cytometry. Appl Microbiol Biotechnol 2020; 104:5547-5562. [DOI: 10.1007/s00253-020-10607-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/24/2020] [Accepted: 04/05/2020] [Indexed: 01/22/2023]
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14
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Bordet F, Joran A, Klein G, Roullier-Gall C, Alexandre H. Yeast-Yeast Interactions: Mechanisms, Methodologies and Impact on Composition. Microorganisms 2020; 8:E600. [PMID: 32326124 PMCID: PMC7232261 DOI: 10.3390/microorganisms8040600] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 12/22/2022] Open
Abstract
During the winemaking process, alcoholic fermentation is carried out by a consortium of yeasts in which interactions occurs. The consequences of these interactions on the wine matrix have been widely described for several years with the aim of controlling the winemaking process as well as possible. In this review, we highlight the wide diversity of methodologies used to study these interactions, and their underlying mechanisms and consequences on the final wine composition and characteristics. The wide variety of matrix parameters, yeast couples, and culture conditions have led to contradictions between the results of the different studies considered. More recent aspects of modifications in the composition of the matrix are addressed through different approaches that have not been synthesized recently. Non-volatile and volatile metabolomics, as well as sensory analysis approaches are developed in this paper. The description of the matrix composition modification does not appear sufficient to explain interaction mechanisms, making it vital to take an integrated approach to draw definite conclusions on them.
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Affiliation(s)
- Fanny Bordet
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, F-21000 Dijon, France-IUVV Equipe VAlMiS, rue Claude Ladrey, BP 27877, 21078 Dijon CEDEX, France
- Lallemand SAS, 19, rue des Briquetiers, BP 59, 31702 Blagnac CEDEX, France
| | - Alexis Joran
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, F-21000 Dijon, France-IUVV Equipe VAlMiS, rue Claude Ladrey, BP 27877, 21078 Dijon CEDEX, France
| | - Géraldine Klein
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, F-21000 Dijon, France-IUVV Equipe VAlMiS, rue Claude Ladrey, BP 27877, 21078 Dijon CEDEX, France
| | - Chloé Roullier-Gall
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, F-21000 Dijon, France-IUVV Equipe VAlMiS, rue Claude Ladrey, BP 27877, 21078 Dijon CEDEX, France
| | - Hervé Alexandre
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, F-21000 Dijon, France-IUVV Equipe VAlMiS, rue Claude Ladrey, BP 27877, 21078 Dijon CEDEX, France
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15
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Huang C, Qian Y, Viana T, Siegumfeldt H, Arneborg N, Larsen N, Jespersen L. The quorum-sensing molecule 2-phenylethanol impaired conidial germination, hyphal membrane integrity and growth of Penicillium expansum and Penicillium nordicum. J Appl Microbiol 2020; 129:278-286. [PMID: 32097516 DOI: 10.1111/jam.14621] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/06/2020] [Accepted: 02/23/2020] [Indexed: 01/23/2023]
Abstract
AIMS The aim of the study was to investigate the antifungal effects of a quorum sensing-molecule, 2-phenylethanol, against the food spoilage moulds Penicillium expansum and Penicillium nordicum. METHODS AND RESULTS Conidial germination of the tested Penicillium spp. (three strains in total) were inhibited by treatments with 2-phenylethanol in a concentration-dependent manner. Germinated conidia was significantly reduced from 4·4-16·7% at 7·5 mmol l-1 and completely inhibited at 15 mmol l-1 2-phenylethanol. Integrity of conidial cell membranes was unaffected by 2-phenylethanol resulting in reversible inhibition pattern of germination. In contrast, membrane permeability of actively growing hyphae was severely compromised, showing 63·5 - 75·7% membrane damage upon treatment with 15 mmol l-1 2-phenylethanol. The overall inhibitory effect of 2-phenylethanol on colony development and growth of P. expansum and P. nordicum was additionally confirmed. CONCLUSIONS 2-phenylethanol inhibits conidial germination and growth of P. expansum and P. nordicum in a nonlethal, reversible and concentration-dependent manner. SIGNIFICANCE AND IMPACT OF THE STUDY The study indicates that 2-phenylethanol can find potential application as an antifungal agent for biological control of moulds in the food industry.
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Affiliation(s)
- C Huang
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Y Qian
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - T Viana
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - H Siegumfeldt
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - N Arneborg
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - N Larsen
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
| | - L Jespersen
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg C, Denmark
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