Predicting and improving complex beer flavor through machine learning.

The perception and appreciation of food flavor depends on many interacting chemical compounds and external factors, and therefore proves challenging to understand and predict. Here, we combine extensive chemical and sensory analyses of 250 different beers to train machine learning models that allow predicting flavor and consumer appreciation. For each beer, we measure over 200 chemical properties, perform quantitative descriptive sensory analysis with a trained tasting panel and map data from over 180,000 consumer reviews to train 10 different machine learning models. The best-performing algorithm, Gradient Boosting, yields models that significantly outperform predictions based on conventional statistics and accurately predict complex food features and consumer appreciation from chemical profiles. Model dissection allows identifying specific and unexpected compounds as drivers of beer flavor and appreciation. Adding these compounds results in variants of commercial alcoholic and non-alcoholic beers with improved consumer appreciation. Together, our study reveals how big data and machine learning uncover complex links between food chemistry, flavor and consumer perception, and lays the foundation to develop novel, tailored foods with superior flavors.

An update on water kefir: Microbiology, composition and production.

Water kefir is a sparkling, slightly acidic fermented beverage produced by fermenting a solution of sucrose, to which dried fruits have been added, with water kefir grains. These gelatinous grains are a symbiotic culture of bacteria and yeast embedded in a polysaccharide matrix. Lactic acid bacteria, yeast and acetic acid bacteria are the primary microbial members of the sugary kefir grain. Amongst other contributions, species of lactic acid bacteria produce the exopolysaccharide matrix from which the kefir grain is formed, while yeast assists the bacteria by a nitrogen source that can be assimilated. Exactly which species predominate within the grain microbiota, however, appears to be dependent on the geographical origin of the grains and the fermentation substrate and conditions. These factors ultimately affect the characteristics of the beverage produced in terms of aroma, flavour, and acidity, for example, but can also be controlled and exploited in the production of a beverage of desired characteristics. The production of water kefir has traditionally occurred on a small scale and the use of defined starter cultures is not commonly practiced. However, as water kefir increases in popularity as a beverage - in part because of consumer lifestyle trends and in part due to water kefir being viewed as a health drink with its purported health benefits - the need for a thorough understanding of the biology and dynamics of water kefir, and for defined and controlled production processes, will ultimately increase. The aim of this review is to provide an update into the current knowledge of water kefir.

Interspecific hybridization facilitates niche adaptation in beer yeast.

Hybridization between species often leads to non-viable or infertile offspring, yet examples of evolutionarily successful interspecific hybrids have been reported in all kingdoms of life. However, many questions on the ecological circumstances and evolutionary aftermath of interspecific hybridization remain unanswered. In this study, we sequenced and phenotyped a large set of interspecific yeast hybrids isolated from brewing environments to uncover the influence of interspecific hybridization in yeast adaptation and domestication. Our analyses demonstrate that several hybrids between Saccharomyces species originated and diversified in industrial environments by combining key traits of each parental species. Furthermore, posthybridization evolution within each hybrid lineage reflects subspecialization and adaptation to specific beer styles, a process that was accompanied by extensive chimerization between subgenomes. Our results reveal how interspecific hybridization provides an important evolutionary route that allows swift adaptation to novel environments.

Physiology of Acetic Acid Bacteria and Their Role in Vinegar and Fermented Beverages.

Acetic acid bacteria (AAB) have, for centuries, been important microorganisms in the production of fermented foods and beverages such as vinegar, kombucha, (water) kefir, and lambic beer. Their unique form of metabolism, known as "oxidative" fermentation, mediates the transformation of a variety of substrates into products, which are of importance in the food and beverage industry and beyond; the most well-known of which is the oxidation of ethanol into acetic acid. Here, a comprehensive review of the physiology of AAB is presented, with particular emphasis on their importance in the production of vinegar and fermented beverages. In addition, particular reference is addressed toward Gluconobacter oxydans due to its biotechnological applications, such as its role in vitamin C production. The production of vinegar and fermented beverages in which AAB play an important role is discussed, followed by an examination of the literature relating to the health benefits associated with consumption of these products. AAB hold great promise for future exploitation, both due to increased consumer demand for traditional fermented beverages such as kombucha, and for the development of new types of products. Further studies on the health benefits related to the consumption of these fermented products and guidelines on assessing the safety of AAB for use as microbial food cultures (starter cultures) are, however, necessary in order to take full advantage of this important group of microorganisms.

Brettanomyces yeasts--From spoilage organisms to valuable contributors to industrial fermentations.

Ever since the introduction of controlled fermentation processes, alcoholic fermentations and Saccharomyces cerevisiae starter cultures proved to be a match made in heaven. The ability of S. cerevisiae to produce and withstand high ethanol concentrations, its pleasant flavour profile and the absence of health-threatening toxin production are only a few of the features that make it the ideal alcoholic fermentation organism. However, in certain conditions or for certain specific fermentation processes, the physiological boundaries of this species limit its applicability. Therefore, there is currently a strong interest in non-Saccharomyces (or non-conventional) yeasts with peculiar features able to replace or accompany S. cerevisiae in specific industrial fermentations. Brettanomyces (teleomorph: Dekkera), with Brettanomyces bruxellensis as the most commonly encountered representative, is such a yeast. Whilst currently mainly considered a spoilage organism responsible for off-flavour production in wine, cider or dairy products, an increasing number of authors report that in some cases, these yeasts can add beneficial (or at least interesting) aromas that increase the flavour complexity of fermented beverages, such as specialty beers. Moreover, its intriguing physiology, with its exceptional stress tolerance and peculiar carbon- and nitrogen metabolism, holds great potential for the production of bioethanol in continuous fermentors. This review summarizes the most notable metabolic features of Brettanomyces, briefly highlights recent insights in its genetic and genomic characteristics and discusses its applications in industrial fermentation processes, such as the production of beer, wine and bioethanol.

Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival.

UNLABELLED: We studied the flocculation mechanism at the molecular level by determining the atomic structures of N-Flo1p and N-Lg-Flo1p in complex with their ligands. We show that they have similar ligand binding mechanisms but distinct carbohydrate specificities and affinities, which are determined by the compactness of the binding site. We characterized the glycans of Flo1p and their role in this binding process and demonstrate that glycan-glycan interactions significantly contribute to the cell-cell adhesion mechanism. Therefore, the extended flocculation mechanism is based on the self-interaction of Flo proteins and this interaction is established in two stages, involving both glycan-glycan and protein-glycan interactions. The crucial role of calcium in both types of interaction was demonstrated: Ca(2+) takes part in the binding of the carbohydrate to the protein, and the glycans aggregate only in the presence of Ca(2+). These results unify the generally accepted lectin hypothesis with the historically first-proposed "Ca(2+)-bridge" hypothesis. Additionally, a new role of cell flocculation is demonstrated; i.e., flocculation is linked to cell conjugation and mating, and survival chances consequently increase significantly by spore formation and by introduction of genetic variability. The role of Flo1p in mating was demonstrated by showing that mating efficiency is increased when cells flocculate and by differential transcriptome analysis of flocculating versus nonflocculating cells in a low-shear environment (microgravity). The results show that a multicellular clump (floc) provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation and mating. IMPORTANCE: Yeast cells can form multicellular clumps under adverse growth conditions that protect cells from harsh environmental stresses. The floc formation is based on the self-interaction of Flo proteins via an N-terminal PA14 lectin domain. We have focused on the flocculation mechanism and its role. We found that carbohydrate specificity and affinity are determined by the accessibility of the binding site of the Flo proteins where the external loops in the ligand-binding domains are involved in glycan recognition specificity. We demonstrated that, in addition to the Flo lectin-glycan interaction, glycan-glycan interactions also contribute significantly to cell-cell recognition and interaction. Additionally, we show that flocculation provides a uniquely organized multicellular ultrastructure that is suitable to induce and accomplish cell mating. Therefore, flocculation is an important mechanism to enhance long-term yeast survival.

A universal fixation method based on quaternary ammonium salts (RNAlater) for omics-technologies: Saccharomyces cerevisiae as a case study.

Genomics, transcriptomics, proteomics and fluxomics are powerful omics-technologies that play a major role in today's research. For each of these techniques good sample quality is crucial. Major factors contributing to the quality of a sample is the actual sampling procedure itself and the way the sample is stored directly after sampling. It has already been described that RNAlater can be used to store tissues and cells in a way that the RNA quality and quantity are preserved. In this paper, we demonstrate that quaternary ammonium salts (RNAlater) are also suitable to preserve and store samples from Saccharomyces cerevisiae for later use with the four major omics-technologies. Moreover, it is shown that RNAlater also preserves the cell morphology and the potential to recover growth, permitting microscopic analysis and yeast cell culturing at a later stage.

The influence of microgravity on invasive growth in Saccharomyces cerevisiae.

This study investigates the effects of microgravity on colony growth and the morphological transition from single cells to short invasive filaments in the model eukaryotic organism Saccharomyces cerevisiae. Two-dimensional spreading of the yeast colonies grown on semi-solid agar medium was reduced under microgravity in the Σ1278b laboratory strain but not in the CMBSESA1 industrial strain. This was supported by the Σ1278b proteome map under microgravity conditions, which revealed upregulation of proteins linked to anaerobic conditions. The Σ1278b strain showed a reduced invasive growth in the center of the yeast colony. Bud scar distribution was slightly affected, with a switch toward more random budding. Together, microgravity conditions disturb spatially programmed budding patterns and generate strain-dependent growth differences in yeast colonies on semi-solid medium.

Flocculation gene variability in industrial brewer's yeast strains.

The brewer's yeast genome encodes a 'Flo' flocculin family responsible for flocculation. Controlled floc formation or flocculation at the end of fermentation is of great importance in the brewing industry since it is a cost-effective and environmental-friendly technique to separate yeast cells from the final beer. FLO genes have the notable capacity to evolve and diverge many times faster than other genes. In actual practice, this genetic variability may directly alter the flocculin structure, which in turn may affect the flocculation onset and/or strength in an uncontrolled manner. Here, 16 ale and lager yeast strains from different breweries, one laboratory Saccharomyces cerevisiae and one reference Saccharomyces pastorianus strain, with divergent flocculation strengths, were selected and screened for characteristic FLO gene sequences. Most of the strains could be distinguished by a typical pattern of these FLO gene markers. The FLO1 and FLO10 markers were only present in five out of the 18 yeast strains, while the FLO9 marker was ubiquitous in all the tested strains. Surprisingly, three strongly flocculating ale yeast strains in this screening also share a typical 'lager' yeast FLO gene marker. Further analysis revealed that a complete Lg-FLO1 allele was present in these ale yeasts. Taken together, this explicit genetic variation between flocculation genes hampers attempts to understand and control the flocculation behavior in industrial brewer's yeasts.

Decrease of aged beer aroma by the reducing activity of brewing yeast.

The flavor profile of beer is subject to changes during storage. Since, possibly, yeast has an influence on flavor stability, the aim of this study was to examine if there is a direct impact of brewing yeast on aged aroma. This was achieved by refermentation of aged beers. It was shown that several aged aroma notes, such as cardboard, ribes, Maillard and Madeira, were removed almost entirely by brewing yeast, independently of the yeast or the beer type. This was explained by the reduction of aldehydes, mainly (E)-2-nonenal, Strecker aldehydes, 5-hydroxymethylfurfural and diacetyl, to their corresponding alcohols. Furthermore, it became evident that the reducing capacity of brewing yeast is high, but that yeast strain and compound specific residual concentrations remained in the refermented beer independently of the initial concentration. Finally, it appeared that aldehydes were not only reduced but also formed during refermentation.

Phenotypic diversity of Flo protein family-mediated adhesion in Saccharomyces cerevisiae.

The Saccharomyces cerevisiae genome encodes a Flo (flocculin) adhesin family responsible for cell-cell and cell-surface adherence. In commonly used laboratory strains, these FLO genes are transcriptionally silent, because of a nonsense mutation in the transcriptional activator FLO8, concealing the potential phenotypic diversity of fungal adhesion. Here, we analyse the distinct adhesion characteristics conferred by each of the five FLO genes in the S288C strain and compare these phenotypes with a strain containing a functional copy of FLO8. Our results show that four FLO genes confer flocculation, but with divergent characteristics such as binding strength, carbohydrate recognition and floc size. Adhesion to agar surfaces, on the other hand, largely depended on two adhesins, Flo10 and Flo11. Expression of any FLO gene caused a significant increase in cell wall hydrophobicity. Nevertheless, the capacity to adhere to plastic surfaces, which is believed to depend on hydrophobic interactions, differed strongly between the adhesins. Restoring Flo8 yielded both flocculation and cell-surface adherence, such as invasive growth, a phenotype not observed when any of the single FLO genes was overexpressed. Taken together, this study reveals how S. cerevisiae carries a small reservoir of FLO genes that allows cells to display a wide variety of adhesive properties.

Evaluation of the glycoside hydrolase activity of a Brettanomyces strain on glycosides from sour cherry (Prunus cerasus L.) used in the production of special fruit beers.

The glycoside hydrolase activity of Saccharomyces cerevisiae and Brettanomyces custersii was examined on sour cherry (Prunus cerasus L.) glycosides with bound volatile compounds. Refermentations by the beta-glucosidase-negative S. cerevisiae strains LD25 and LD40 of sour cherry juice-supplemented beer demonstrated only a moderate increase of volatiles. In contrast, the beta-glucosidase-positive B. custersii strain LD72 showed a more pronounced activity towards glycosides with aliphatic alcohols, aromatic compounds and terpenoid alcohols. Important contributors to sour cherry aroma such as benzaldehyde, linalool and eugenol were released during refermentation as shown by analytical tools. A gradually increasing release was observed during refermentations by B. custersii when whole sour cherries, sour cherry pulp or juice were supplemented in the beer. Refermentations with whole sour cherries and with sour cherry stones demonstrated an increased formation of benzyl compounds. Thus, amygdalin was partially hydrolysed, and a large part of the benzaldehyde formed was mainly reduced to benzyl alcohol and some further esterified to benzyl acetate. These findings demonstrate the importance and interesting role of certain Brettanomyces species in the production of fruit lambic beers such as 'Kriek'.

Furfuryl ethyl ether: important aging flavor and a new marker for the storage conditions of beer.

Recently, it was reported that furfuryl ethyl ether is an important flavor compound indicative of beer storage and aging conditions. A study of the reaction mechanism indicates that furfuryl ethyl ether is most likely formed by protonation of furfuryl alcohol or furfuryl acetate followed by S(N)2-substitution of the leaving group by the nucleophilic ethanol. For the reaction in beer, a pseudo-first-order reaction kinetics was derived. A close correlation was found between the values predicted by the kinetic model and the actual furfuryl ethyl ether concentration evolution during storage of beer. Furthermore, 10 commercial beers of different types, aged during 4 years in natural conditions, were analyzed, and it was found that the furfuryl ethyl ether flavor threshold was largely exceeded in each type of beer. In these natural aging conditions, lower pH, darker color, and higher alcohol content were factors that enhanced furfuryl ethyl ether formation. On the other hand, sulfite clearly reduced furfuryl ethyl ether formation. All results show that the furfuryl ethyl ether concentration is an excellent time-temperature integrator for beer storage.