Sulfur dioxide response of Brettanomyces bruxellensis strains isolated from Greek wine

Synthesis of an autochthonous microbial community by analyzing the core microorganisms responsible for the critical flavor of bran vinegar

Traditional bran vinegar brewing unfolds through natural fermentation, a process driven by spontaneous microbial activity. The unique metabolic activities of various microorganisms lead to distinct flavors and qualities in each batch of vinegar, making it challenging to consistently achieve the desired characteristic flavor compounds. Therefore, identifying the critical microbial species responsible for flavor production and designing starter cultures with improved fermentation efficiency and characteristic flavors are effective methods to address this discrepancy. In this study, 11 core functional microbial species affecting the fermentation flavor of Sichuan shai vinegar (Cupei were placed outside solarization and night-dew for more than one year, and vinegar was the liquid leached from Cupei) (SSV), were revealed by combining PacBio full-length diversity sequencing based on previous metagenomics. The effects of environmental factors and microbial interactions on the growth of 11 microorganisms during fermentation were verified using fermentation experiments. Ultimately, the microbial community was strategically synthesized using a 'top-down' approach, successfully replicating the distinctive flavor profile of Sichuan shai vinegar (SSV). The results showed that the interaction between microorganisms and environmental factors affected microorganism growth. Compared with traditional fermentation, the synthetic microbial community's vinegar-fermented grains (Cupei) can reproduce the key flavor of SSV and is conducive to the production of amino acids. In this study, the key flavor of SSV was reproduced through rational design of the synthetic microbial community. This achievement holds profound significance for the broader application of microbiome assembly strategies in the realm of fermented foods.

Molecular approaches improving our understanding of Brettanomyces physiology

Brettanomyces species and particularly B. bruxellensis as the most studied representative, are strongly linked to industrial fermentation processes. This association is considered either positive or undesirable depending on the industry. While in some brewing applications and in kombucha production Brettanomyces yeasts contribute to the flavour and aroma profile of these beverages, in winemaking and bioethanol production Brettanomyces is considered a spoilage or contaminant microorganism. Nevertheless, understanding Brettanomyces biology and metabolism in detail will benefit all industries. This review discusses recent molecular biology tools including genomics, transcriptomics and genetic engineering techniques that can improve our understanding of Brettanomyces physiology and how these approaches can be used to make the industrial potential of this species a reality.

Brettanomyces bruxellensis: Overview of the genetic and phenotypic diversity of an anthropized yeast

Human-associated microorganisms are ideal models to study the impact of environmental changes on species evolution and adaptation because of their small genome, short generation time, and their colonization of contrasting and ever-changing ecological niches. The yeast Brettanomyces bruxellensis is a good example of organism facing anthropogenic-driven selective pressures. It is associated with fermentation processes in which it can be considered either as a spoiler (e.g. winemaking, bioethanol production) or as a beneficial microorganism (e.g. production of specific beers, kombucha). Besides its industrial interests, noteworthy parallels and dichotomies with Saccharomyces cerevisiae propelled B. bruxellensis as a valuable complementary yeast model. In this review, we emphasize that the broad genetic and phenotypic diversity of this species is only beginning to be uncovered. Population genomic studies have revealed the co-existence of auto- and allotriploidization events with different evolutionary outcomes. The different diploid, autotriploid and allotriploid subpopulations are associated with specific fermented processes, suggesting independent adaptation events to anthropized environments. Phenotypically, B. bruxellensis is renowned for its ability to metabolize a wide variety of carbon and nitrogen sources, which may explain its ability to colonize already fermented environments showing low-nutrient contents. Several traits of interest could be related to adaptation to human activities (e.g. nitrate metabolization in bioethanol production, resistance to sulphite treatments in winemaking). However, phenotypic traits are insufficiently studied in view of the great genomic diversity of the species. Future work will have to take into account strains of varied substrates, geographical origins as well as displaying different ploidy levels to improve our understanding of an anthropized yeast's phenotypic landscape.

Fungal diversity on brewery filling hall surfaces and quality control samples

Breweries produce an increasing selection of beer and nonbeer beverages. Yeast and filamentous fungi may compromise quality and safety of these products in several ways. Recent studies on fungal communities in breweries are scarce and mostly conducted with culture-dependent methods. We explored fungal diversity in the production of alcoholic and nonalcoholic beverages in four breweries. Samples were taken for next generation sequencing (NGS) at the key contamination sites in 10 filling lines. Moreover, fungal isolates were identified in 68 quality control samples taken from raw materials, filling line surfaces, air, and products. NGS gave a comprehensive view of fungal diversity on filling line surfaces. The surface-attached communities mainly contained ascomycetous fungi. Depending on the site, the dominant genera included Candida, Saccharomyces, Torulaspora, Zygosaccharomyces, Alternaria, Didymella, and Exophiala. Sanger sequencing revealed 28 and 27 species of yeast and filamentous fungi, respectively, among 91 isolates. The most common species Saccharomyces cerevisiae, Zygosaccharomyces rouxii, and Wickerhamomuces anomalus were detected throughout production. Filling line surface and air samples showed the greatest diversity of yeast and filamentous fungi, respectively. The isolates of the most common yeast genera Candida, Pichia, Saccharomyces, and Wickerhamomyces showed low spoilage abilities in carbonated, chemically preserved drinks but could grow in products with reduced hurdles. Preservative resistant yeasts were rare, belonging to the species Dekkera bruxellensis, Pichia manschurica, and Zygosaccharomyces bailii. Penicillium spp. were dominant filamentous fungi. The results of this study help to evaluate spoilage risks caused by fungal contaminants detected in breweries.

Prediction of Genetic Groups within Brettanomyces bruxellensis through Cell Morphology Using a Deep Learning Tool

Brettanomyces bruxellensis is described as a wine spoilage yeast with many mainly strain-dependent genetic characteristics, bestowing tolerance against environmental stresses and persistence during the winemaking process. Thus, it is essential to discriminate B. bruxellensis isolates at the strain level in order to predict their stress resistance capacities. Few predictive tools are available to reveal intraspecific diversity within B. bruxellensis species; also, they require expertise and can be expensive. In this study, a Random Amplified Polymorphic DNA (RAPD) adapted PCR method was used with three different primers to discriminate 74 different B. bruxellensis isolates. High correlation between the results of this method using the primer OPA-09 and those of a previous microsatellite analysis was obtained, allowing us to cluster the isolates among four genetic groups more quickly and cheaply than microsatellite analysis. To make analysis even faster, we further investigated the correlation suggested in a previous study between genetic groups and cell polymorphism using the analysis of optical microscopy images via deep learning. A Convolutional Neural Network (CNN) was trained to predict the genetic group of B. bruxellensis isolates with 96.6% accuracy. These methods make intraspecific discrimination among B. bruxellensis species faster, simpler and less costly. These results open up very promising new perspectives in oenology for the study of microbial ecosystems.

Assessing the Biofilm Formation Capacity of the Wine Spoilage Yeast Brettanomyces bruxellensis through FTIR Spectroscopy

Brettanomyces bruxellensis is a wine spoilage yeast known to colonize and persist in production cellars. However, knowledge on the biofilm formation capacity of B. bruxellensis remains limited. The present study investigated the biofilm formation of 11 B. bruxellensis strains on stainless steel coupons after 3 h of incubation in an aqueous solution. FTIR analysis was performed for both planktonic and attached cells, while comparison of the obtained spectra revealed chemical groups implicated in the biofilm formation process. The increased region corresponding to polysaccharides and lipids clearly discriminated the obtained spectra, while the absorption peaks at the specific wavenumbers possibly reveal the presence of β-glucans, mannas and ergosterol. Unsupervised clustering and supervised classification were employed to identify the important wavenumbers of the whole spectra. The fact that all the metabolic fingerprints of the attached versus the planktonic cells were similar within the same cell phenotype class and different between the two phenotypes, implies a clear separation of the cell phenotype; supported by the results of the developed classification model. This study represents the first to succeed at applying a non-invasive technique to reveal the metabolic fingerprint implicated in the biofilm formation capacity of B. bruxellensis, underlying the homogenous mechanism within the yeast species.

Morphological and physiological changes in Lentilactobacillus hilgardii cells after cold plasma treatment

Atmospheric cold plasma (ACP) inactivation of Lentilactobacillus hilgardii was investigated. Bacteria were exposed to ACP dielectric barrier discharge with helium and oxygen as working gases for 5, 10, and 15 min. The innovative approach in our work for evaluation of bacterial survival was the use in addition to the classical plate culture method also flow cytometry which allowed the cells to be sorted and revealed different physiological states after the plasma treatment. Results showed total inhibition of bacterial growth after 10-min of ACP exposure. However, the analysis of flow cytometry demonstrated the presence of 14.4% of active cells 77.5% of cells in the mid-active state and 8.1% of dead cells after 10 min. In addition, some of the cells in the mid-active state showed the ability to grow again on culture medium, thus confirming the hypothesis of induction of VBNC state in L .hilgardii cells by cold plasma. In turn, atomic force microscopy (AFM) which was used to study morphological changes in L. hilgardii after plasma treatment at particular physiological states (active, mid-active, dead), showed that the surface roughness of the mid-active cell (2.70 ± 0.75 nm) was similar to that of the control sample (2.04 ± 0.55 nm). The lack of considerable changes on the cell surface additionally explains the effective cell resuscitation. To the best of our knowledge, AFM was used for the first time in this work to analyze cells which have been sorted into subpopulations after cold plasma treatment and this is the first work indicating the induction of VBNC state in L. hilgardii cells after exposure to cold plasma.

Effect of Thermosonication and Physicochemical Properties of Wine on Culturability, Viability, and Metabolic Activity of Brettanomyces bruxellensis Yeast in Red Wines

The aim of this research was to investigate the short- and long-term effects of thermosonication and different physicochemical properties of wine on culturability, viability, and metabolic activity of Brettanomyces bruxellensis yeast. Thermosonication was conducted at 43 °C during 1, 2, and 3 min, while wine variations included several pH, alcohol, and sugar levels. Cell culturability and viability were determined immediately after treatment and during 90 days of storage, while metabolic activity was determined after 90 days of storage. Results showed that, although culturability was not confirmed in dry wines immediately after 3 min of treatment, thermosonication did not result in complete inactivation of the B. bruxellensis population. Herein, the first evidence of a viable but not culturable (VBNC) state of B. bruxellensis after thermosonication exposure was observed. Moreover, thermosonication reduced the production of volatile phenols. Obtained results suggest application of thermosonication for reduction of the B. bruxellensis population only in early stages of wine contamination.

New molecularly imprinted polymers for reducing negative volatile phenols in red wine with low impact on wine colour

4-Ethylphenol (4-EP) and 4-ethylguaiacol (4-EG) formation in red wines by Dekkera/Brettanomyces yeasts reduce significantly wine consumer's acceptability. Polymers with specific adsorption for volatile phenols (VPs) could be a valuable tool for wine producers for removing this negative sensory defect. In this work, a new molecularly imprinted polymer (MIP) was synthesised using ethylene glycol dimethacrylate (EDMA) as cross-linker and ethylene glycol methyl ether acrylate as functional monomers. Although there was observed a competitive binding of the more abundant structurally related phenolic compounds of the wine matrix, it was still able to reduce 38 to 63% the wine VPs, depending on the wine VPs levels, presenting higher performance than the respective non-imprinted polymers (NIP). Sensory analysis of the MIP treated wine resulted in a significant decrease in the phenolic attribute and significant increase of the fruity and floral attributes, with no significant differences in the wine colour perceived by the expert panel. The sensory improvement of the MIP was significantly higher than that observed for the correspondent NIP.

Brettanomyces bruxellensis wine isolates show high geographical dispersal and long persistence in cellars

Brettanomyces bruxellensis is the main wine spoiler yeast all over the world, yet the structure of the populations associated with winemaking remains elusive. In this work, we considered 1411 wine isolates from 21 countries that were genotyped using twelve microsatellite markers. We confirmed that B. bruxellensis isolates from wine environments show high genetic diversity, with 58 and 42% of putative triploid and diploid individuals respectively distributed in 5 main genetic groups. The distribution in the genetic groups varied greatly depending on the country and/or the wine-producing region. However, the two possible triploid wine groups showing sulfite resistance/tolerance were identified in almost all regions/countries. Genetically identical isolates were also identified. The analysis of these clone groups revealed that a given genotype could be isolated repeatedly in the same winery over decades, demonstrating unsuspected persistence ability. Besides cellar residency, a great geographic dispersal was also evidenced, with some genotypes isolated in wines from different continents. Finally, the study of old isolates and/or isolates from old vintages revealed that only the diploid groups were identified prior 1990 vintages. The putative triploid groups were identified in subsequent vintages, and their proportion has increased steadily these last decades, suggesting adaptation to winemaking practices such as sulfite use. A possible evolutionary scenario explaining these results is discussed.