Fermentative and metabolic screening of candidate yeast strains hybridisable with Saccharomyces cerevisiae for beer production optimisation

Yeast optimisation has been crucial in improving the quality and efficiency of beer production, one of the world's most widely consumed beverages. In this context, rare mating hybridisation is a promising technique for yeast optimization to generate novel and improved non-GMO strains. The limitation of this technique is the lack of knowledge and comparable data on yeast strains hybridisable to Saccharomyces cerevisiae, probably the most important yeast species in beer production. Yeast from the genera Saccharomyces, Naumovozyma, Nakaseomyces and Kazachstania have been described to be able to form hybrids with S. cerevisiae. In the present study, 242 yeast strains were analysed under brewing conditions, including Saccharomyces species (S. cerevisiae, S. kudriavzevii, S. uvarum, S. eubayanus, S. paradoxus, S. mikatae, S. jurei and S. arboricola) and non-Saccharomyces species (Naumovozyma, Nakaseomyces and Kazaschtania), representing the full genetic variability (species and subpopulations) described up to the start of the study. The fermentation profile was analysed by monitoring weight loss during fermentation to determine kinetic parameters and CO2 production. Metabolic analysis was performed to determine the concentration of sugars (maltotriose, maltose and glucose), alcohols (ethanol, glycerol and 2,3-butanediol) and organic acids (malic acid, succinic acid and acetic acid). Maltose and maltotriose are the predominant sugars in beer wort. The ability to consume these sugars determines the characteristics of the final product. Dataset comparisons were then made at species, subpopulation and isolation source level. The results obtained in this study demonstrate the great phenotypic variability that exists within the genus Saccharomyces and within each species of this genus, which could be useful in the generation of optimised brewing hybrids. Yeasts with different fermentative capacities and fermentative behaviours can be found under brewing conditions. S. cerevisiae, S. uvarum and S. eubayanus are the species that contain strains with similar fermentation performance to commercial strains.

Evolution-aided improvement of the acid tolerance of Levilactobacillus brevis and its application in sourdough fermentation

Levilactobacillus brevis is crucial in food fermentation, particularly in sourdough production. However, the cultivation of L. brevis faces a challenge with accumulation of lactic acid, a major inhibitor. We aimed to increase the acid tolerance of L. brevis, an industrial strain for sourdough fermentation. We used the adaptive laboratory evolution (ALE) to obtain lactic acid tolerant strains. The evolved strain's fermentation and metabolite profiles, alongside sensory evaluation, were compared with the parental strain by using various analytical techniques. The ALE approach increased lactic acid tolerance in the evolved strain showing an increased growth rate by 1.1 and 1.9 times higher than the parental strain at pH 4.1 and 6.5, respectively. Comprehensive analyses demonstrated its potential application in sourdough fermentation, promising reduced downstream costs. The evolved strain, free from genetically modified organisms concerns, has great potential for industrial use by exhibiting enhanced growth in acidic conditions without affecting consumers' bread preferences.

Recent Advances and Multiple Strategies of Monoterpenoid Overproduction in Saccharomyces cerevisiae and Yarrowia lipolytica

Monoterpenoids are an important subclass of terpenoids that play important roles in the energy, cosmetics, pharmaceuticals, and fragrances fields. With the development of biotechnology, microbial synthesis of monoterpenoids has received great attention. Yeasts such Saccharomyces cerevisiae and Yarrowia lipolytica are emerging as potential hosts for monoterpenoids production because of unique advantages including rapid growth cycles, mature gene editing tools, and clear genetic background. Recently, advancements in metabolic engineering and fermentation engineering have significantly enhanced the accumulation of monoterpenoids in cell factories. First, this review introduces the biosynthetic pathway of monoterpenoids and comprehensively summarizes the latest production strategies, which encompass enhancing precursor flux, modulating the expression of rate-limited enzymes, suppressing competitive pathway flux, mitigating cytotoxicity, optimizing substrate utilization, and refining the fermentation process. Subsequently, this review introduces four representative monoterpenoids. Finally, we outline the future prospects for efficient construction cell factories tailored for the production of monoterpenoids and other terpenoids.

Breeding of high-tolerance yeast by adaptive evolution and high-gravity brewing of mutant

BACKGROUND

Ethanol and osmotic stresses are the major limiting factors for brewing strong beer with high-gravity wort. Breeding of yeast strains with high osmotic and ethanol tolerance and studying very-high-gravity (VHG) brewing technology is of great significance for brewing strong beer.

RESULTS

This study used an optimized microbial microdroplet culture (MMC) system for adaptive laboratory evolution (ALE) of Saccharomyces cerevisiae YN81 to improve its tolerance to osmotic and ethanol stress. Meanwhile, we investigated the VHG and VHG with added ethanol (VHGAE) brewing processes for the evolved mutants in brewing strong beer. The results showed that three evolved mutants were obtained; among them, the growth performance of YN81mc-8.3 under 300, 340, 380, 420 and 460 g L-1 sucrose stresses was greater than that of the other strains. The ethanol tolerance of YN81mc-8.3 was 12%, which was 20% higher than that of YN81. During strong-beer brewing in a 100 L cylindrical cone-bottom tank, the sugar utilization and ethanol yield of YN81mc-8.3 outperformed those of YN81 in both the VHG and VHGAE brewing processes. Measurement of the diacetyl concentration showed that YN81mc-8.3 had a stronger diacetyl reduction ability; in particular, the real degree of fermentation of beers brewed by YN81mc-8.3 in VHG and VHGAE brewing processes was 75.35% and 66.71%, respectively - higher than those of the two samples brewed by YN81. Meanwhile, the visual, olfactive and gustative properties of the strong beer produced by YN81mc-8.3 were better than those of the other beers.

CONCLUSION

In this study, the mutant YN81mc-8.3 and the VHGAE brewing process were optimal and represented a better alternative strong-beer brewing process. © 2023 Society of Chemical Industry.

Domestication signatures in the non-conventional yeast Lachancea cidri

Evaluating domestication signatures beyond model organisms is essential for a thorough understanding of the genotype-phenotype relationship in wild and human-related environments. Structural variations (SVs) can significantly impact phenotypes playing an important role in the physiological adaptation of species to different niches, including during domestication. A detailed characterization of the fitness consequences of these genomic rearrangements, however, is still limited in non-model systems, largely due to the paucity of direct comparisons between domesticated and wild isolates. Here, we used a combination of sequencing strategies to explore major genomic rearrangements in a Lachancea cidri yeast strain isolated from cider (CBS2950) and compared them to those in eight wild isolates from primary forests. Genomic analysis revealed dozens of SVs, including a large reciprocal translocation (~16 kb and 500 kb) present in the cider strain, but absent from all wild strains. Interestingly, the number of SVs was higher relative to single-nucleotide polymorphisms in the cider strain, suggesting a significant role in the strain's phenotypic variation. The set of SVs identified directly impacts dozens of genes and likely underpins the greater fermentation performance in the L. cidri CBS2950. In addition, the large reciprocal translocation affects a proline permease (PUT4) regulatory region, resulting in higher PUT4 transcript levels, which agrees with higher ethanol tolerance, improved cell growth when using proline, and higher amino acid consumption during fermentation. These results suggest that SVs are responsible for the rapid physiological adaptation of yeast to a human-related environment and demonstrate the key contribution of SVs in adaptive fermentative traits in non-model species.IMPORTANCEThe exploration of domestication signatures associated with human-related environments has predominantly focused on studies conducted on model organisms, such as Saccharomyces cerevisiae, overlooking the potential for comparisons across other non-Saccharomyces species. In our research, employing a combination of long- and short-read data, we found domestication signatures in Lachancea cidri, a non-model species recently isolated from fermentative environments in cider in France. The significance of our study lies in the identification of large array of major genomic rearrangements in a cider strain compared to wild isolates, which underly several fermentative traits. These domestication signatures result from structural variants, which are likely responsible for the phenotypic differences between strains, providing a rapid path of adaptation to human-related environments.

The origins of the Guinness stout yeast

Beer is made via the fermentation of an aqueous extract predominantly composed of malted barley flavoured with hops. The transforming microorganism is typically a single strain of Saccharomyces cerevisiae, and for the majority of major beer brands the yeast strain is a unique component. The present yeast used to make Guinness stout brewed in Dublin, Ireland, can be traced back to 1903, but its origins are unknown. To that end, we used Illumina and Nanopore sequencing to generate whole-genome sequencing data for a total of 22 S. cerevisiae yeast strains: 16 from the Guinness collection and 6 other historical Irish brewing. The origins of the Guinness yeast were determined with a SNP-based analysis, demonstrating that the Guinness strains occupy a distinct group separate from other historical Irish brewing yeasts. Assessment of chromosome number, copy number variation and phenotypic evaluation of key brewing attributes established Guinness yeast-specific SNPs but no specific chromosomal amplifications. Our analysis also demonstrated the effects of yeast storage on phylogeny. Altogether, our results suggest that the Guinness yeast used today is related to the first deposited Guinness yeast; the 1903 Watling Laboratory Guinness yeast.

The potential for Scotch Malt Whisky flavour diversification by yeast

Scotch Whisky, a product of high importance to Scotland, has gained global approval for its distinctive qualities derived from the traditional production process, which is defined in law. However, ongoing research continuously enhances Scotch Whisky production and is fostering a diversification of flavour profiles. To be classified as Scotch Whisky, the final spirit needs to retain the aroma and taste of 'Scotch'. While each production step contributes significantly to whisky flavour-from malt preparation and mashing to fermentation, distillation, and maturation-the impact of yeast during fermentation is crucially important. Not only does the yeast convert the sugar to alcohol, it also produces important volatile compounds, e.g. esters and higher alcohols, that contribute to the final flavour profile of whisky. The yeast chosen for whisky fermentations can significantly influence whisky flavour, so the yeast strain employed is of high importance. This review explores the role of yeast in Scotch Whisky production and its influence on flavour diversification. Furthermore, an extensive examination of nonconventional yeasts employed in brewing and winemaking is undertaken to assess their potential suitability for adoption as Scotch Whisky yeast strains, followed by a review of methods for evaluating new yeast strains.

Heterotypic stress-induced adaptive evolution enhances freeze-drying tolerance and storage stability of Leuconostoc mesenteroides WiKim33

Lactic acid bacteria (LAB) are currently being investigated for their potential use as probiotics and starter cultures. Researchers have developed powdering processes for the commercialization of LAB. Previous studies have focused on identifying innovative cryoprotective agents and freeze-drying (FD) techniques to enhance the stability of LAB. In this study, adaptive laboratory evolution (ALE) was employed to develop a strain with high FD tolerance and enhanced storage stability. Leuconostoc mesenteroids WiKim33 was subjected to heterotypic shock (heat and osmosis shock) to induce the desired phenotype and genotype. An FD-tolerant enhanced Leu. mesenteroides WiKim33 strain (ALE50) was obtained, which harbored a modified fatty acid composition and cell envelope characteristics. Specifically, ALE50 showed a lower unsaturated fatty acid (UFA)/saturated fatty acid (SFA) ratio and a higher cyclic fatty acid (CFA) composition. Moreover, the exopolysaccharide (EPS) thickness increased significantly by 331% compared to that of the wild type (WT). FD tolerance, which was evaluated using viability testing after FD, was enhanced by 33.4%. Overall, we demonstrated the feasibility of ALE to achieve desirable characteristics and provided insights into the mechanisms underlying increased FD tolerance.

Engineering the Metabolic Landscape of Microorganisms for Lignocellulosic Conversion

Bacteria and yeast are being intensively used to produce biofuels and high-added-value products by using plant biomass derivatives as substrates. The number of microorganisms available for industrial processes is increasing thanks to biotechnological improvements to enhance their productivity and yield through microbial metabolic engineering and laboratory evolution. This is allowing the traditional industrial processes for biofuel production, which included multiple steps, to be improved through the consolidation of single-step processes, reducing the time of the global process, and increasing the yield and operational conditions in terms of the desired products. Engineered microorganisms are now capable of using feedstocks that they were unable to process before their modification, opening broader possibilities for establishing new markets in places where biomass is available. This review discusses metabolic engineering approaches that have been used to improve the microbial processing of biomass to convert the plant feedstock into fuels. Metabolically engineered microorganisms (MEMs) such as bacteria, yeasts, and microalgae are described, highlighting their performance and the biotechnological tools that were used to modify them. Finally, some examples of patents related to the MEMs are mentioned in order to contextualize their current industrial use.

Sour Beer as Bioreservoir of Novel Craft Ale Yeast Cultures

The increasing demand for craft beer is driving the search for novel ale yeast cultures from brewing-related wild environments. The focus of bioprospecting for craft cultures is to identify feral yeasts suitable to imprint unique sensorial attributes onto the final product. Here, we integrated phylogenetic, genotypic, genetic, and metabolomic techniques to demonstrate that sour beer during aging in wooden barrels is a source of suitable craft ale yeast candidates. In contrast to the traditional lambic beer maturation phase, during the aging of sour-matured production-style beer, different biotypes of Saccharomyces cerevisiae dominated the cultivable in-house mycobiota, which were followed by Pichia membranifaciens, Brettanomyces bruxellensis, and Brettanomyces anomalus. In addition, three putative S. cerevisiae × Saccharomyces uvarum hybrids were identified. S. cerevisiae feral strains sporulated, produced viable monosporic progenies, and had the STA1 gene downstream as a full-length promoter. During hopped wort fermentation, four S. cerevisiae strains and the S. cerevisiae × S. uvarum hybrid WY213 exceeded non-Saccharomyces strains in fermentative rate and ethanol production except for P. membranifaciens WY122. This strain consumed maltose after a long lag phase, in contrast to the phenotypic profile described for the species. According to the STA1+ genotype, S. cerevisiae partially consumed dextrin. Among the volatile organic compounds (VOCs) produced by S. cerevisiae and the S. cerevisiae × S. uvarum hybrid, phenylethyl alcohol, which has a fruit-like aroma, was the most prevalent. In conclusion, the strains characterized here have relevant brewing properties and are exploitable as indigenous craft beer starters.

Production and sensory analysis of grape flavoured beer by co-fermentation of an industrial and a genetically modified laboratory yeast strain

The so-called "craft beer revolution" has increased the demand for new styles of beers, often with new ingredients like flavour extracts. In recent years, synthetic biology has realized the production of a plethora of plant secondary metabolites in microbial hosts, which could provide an alternative source for these compounds. In this study, we selected a in situ flavour production approach for grape flavour addition. We used an O-methyl anthranilate (OmANT) producing laboratory Saccharomyces cerevisiae strain in co-fermentations with an industrial beer yeast strain WLP644. The laboratory strain provided an ease of genetic manipulation and the desirable properties of the WLP644 strain were not modified in this approach. In shake flasks, a 10:90 ratio of the yeasts produced grape flavoured beer with the yeast produced flavour compound in a range normally used for flavoured beverages. Hopped and unhopped beers were analysed by VTT's trained sensory panel and with olfactory GC-MS. OmANT was successfully detected from the beers as a floral odour and flavour. Moreover, no off-flavours were detected and aroma profiles outside the grape flavour were rather similar. These results indicate that the co-fermentation principle is a suitable approach to change the flavour profiles of beers with a simple yeast strain drop-in approach.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00217-023-04274-1.

Improving CRISPR-Cas9 mediated genome integration in interspecific hybrid yeasts

Saccharomyces pastorianus is not a classical taxon, it is an interspecific hybrid resulting from the cross of Saccharomyces cerevisiae and Saccharomyces eubayanus. Exhibiting heterosis for phenotypic traits such as wort α-oligosaccharide consumption and fermentation at low temperature, it has been domesticated to become the main workhorse of the brewing industry. Although CRISPR-Cas9 has been shown to be functional in S. pastorianus, repair of CRISPR- induced double strand break is unpredictable and preferentially uses the homoeologous chromosome as template, preventing targeted introduction of the desired repair construct. Here, we demonstrate that lager hybrids can be edited with near 100% efficiency at carefully selected landing sites on the chimeric SeScCHRIII. The landing sites were systematically selected and evaluated for (i) absence of loss of heterozygosity upon CRISPR-editing, (ii) efficiency of the gRNA, and (iii) absence of effect on strain physiology. Successful examples of highly efficient single and double gene integration illustrated that genome editing can be applied in interspecies hybrids, paving the way to a new impulse to lager yeast strain development. DATA AVAILABILITY: Data underlying graphs and figures found in this manuscript are deposited at the 4TU research dat center (https://data.4tu.nl/info/en/) and available through the doi: 10.4121/21648329.

Contributions of Adaptive Laboratory Evolution towards the Enhancement of the Biotechnological Potential of Non-Conventional Yeast Species

Changes in biological properties over several generations, induced by controlling short-term evolutionary processes in the laboratory through selective pressure, and whole-genome re-sequencing, help determine the genetic basis of microorganism's adaptive laboratory evolution (ALE). Due to the versatility of this technique and the imminent urgency for alternatives to petroleum-based strategies, ALE has been actively conducted for several yeasts, primarily using the conventional species Saccharomyces cerevisiae, but also non-conventional yeasts. As a hot topic at the moment since genetically modified organisms are a debatable subject and a global consensus on their employment has not yet been attained, a panoply of new studies employing ALE approaches have emerged and many different applications have been exploited in this context. In the present review, we gathered, for the first time, relevant studies showing the ALE of non-conventional yeast species towards their biotechnological improvement, cataloging them according to the aim of the study, and comparing them considering the species used, the outcome of the experiment, and the employed methodology. This review sheds light on the applicability of ALE as a powerful tool to enhance species features and improve their performance in biotechnology, with emphasis on the non-conventional yeast species, as an alternative or in combination with genome editing approaches.

A review of yeast: High cell-density culture, molecular mechanisms of stress response and tolerance during fermentation

Yeast is widely used in the fermentation industry, and the major challenges in fermentation production system are high capital cost and low reaction rate. High cell-density culture is an effective method to increase the volumetric productivity of the fermentation process, thus making the fermentation process faster and more robust. During fermentation, yeast is subjected to various environmental stresses, including osmotic, ethanol, oxidation, and heat stress. To cope with these stresses, yeast cells need appropriate adaptive responses to acquire stress tolerances to prevent stress-induced cell damage. Since a single stressor can trigger multiple effects, both specific and nonspecific effects, general and specific stress responses are required to achieve comprehensive protection of cells. Since all these stresses disrupt protein structure, the upregulation of heat shock proteins and trehalose genes is induced when yeast cells are exposed to stress. A better understanding of the research status of yeast HCDC and its underlying response mechanism to various stresses during fermentation is essential for designing effective culture control strategies and improving the fermentation efficiency and stress resistance of yeast.

Adaptive Laboratory Evolution of Yeasts for Aroma Compound Production

Aroma compounds are important in the food and beverage industry, as they contribute to the quality of fermented products. Yeasts produce several aroma compounds during fermentation. In recent decades, production of many aroma compounds by yeasts obtained through adaptive laboratory evolution has become prevalent, due to consumer demand for yeast strains in the industry. This review presents general aspects of yeast, aroma production and adaptive laboratory evolution and focuses on the recent advances of yeast strains obtained by adaptive laboratory evolution to enhance the production of aroma compounds.

Sustainable production of astaxanthin in microorganisms: the past, present, and future

Astaxanthin (3,3'-dihydroxy-4,4'-diketo-β-carotene) is a type of C40 carotenoid with remarkable antioxidant characteristics, showing significant application prospects in many fields. Traditionally, the astaxanthin is mainly obtained from chemical synthesis and natural acquisition, with both approaches having many limitations and not capable of meeting the growing market demand. In order to cope with these challenges, novel techniques, e.g., the innovative cell engineering strategies, have been developed to increase the astaxanthin production. In this review, we first elaborated the biosynthetic pathway of astaxanthin, with the key enzymes and their functions discussed in the metabolic process. Then, we summarized the conventional, non-genetic strategies to promote the production of astaxanthin, including the methods of exogenous additives, mutagenesis, and adaptive evolution. Lastly, we reviewed comprehensively the latest studies on the synthesis of astaxanthin in various recombinant microorganisms based on the concept of microbial cell factory. Furthermore, we have proposed several novel technologies for improving the astaxanthin accumulation in several model species of microorganisms.

Probiotic Yeast Saccharomyces: Back to Nature to Improve Human Health

Saccharomyces cerevisiae var. boulardii is best known for its treatment efficacy against different gastrointestinal diseases. This probiotic yeast can significantly protect the normal microbiota of the human gut and inhibit the pathogenicity of different diarrheal infections. Several clinical investigations have declared S. cerevisiae var. boulardii a biotherapeutic agent due to its antibacterial, antiviral, anti-carcinogenic, antioxidant, anti-inflammatory and immune-modulatory properties. Oral or intramuscular administration of S. cerevisiae var. boulardii can remarkably induce health-promoting effects in the host body. Different intrinsic and extrinsic factors are responsible for its efficacy against acute and chronic gut-associated diseases. This review will discuss the clinical and beneficial effects of S. cerevisiae var. boulardii in the treatment and prevention of different metabolic diseases and highlight some of its health-promising properties. This review article will provide fundamental insights for new avenues in the fields of biotherapeutics, antimicrobial resistance and one health.

Yeasts from temperate forests

Yeasts are ubiquitous in temperate forests. While this broad habitat is well-defined, the yeasts inhabiting it and their life cycles, niches, and contributions to ecosystem functioning are less understood. Yeasts are present on nearly all sampled substrates in temperate forests worldwide. They associate with soils, macroorganisms, and other habitats, and no doubt contribute to broader ecosystem-wide processes. Researchers have gathered information leading to hypotheses about yeasts' niches and their life cycles based on physiological observations in the laboratory as well as genomic analyses, but the challenge remains to test these hypotheses in the forests themselves. Here we summarize the habitat and global patterns of yeast diversity, give some information on a handful of well-studied temperate forest yeast genera, discuss the various strategies to isolate forest yeasts, and explain temperate forest yeasts' contributions to biotechnology. We close with a summary of the many future directions and outstanding questions facing researchers in temperate forest yeast ecology. Yeasts present an exciting opportunity to better understand the hidden world of microbial ecology in this threatened and global habitat.

Nutritional and Volatile Characterisation of Milk Inoculated with Thermo-Tolerant Lactobacillus bulgaricus through Adaptive Laboratory Evolution

In this study, thermo-tolerant strain of Lactobacillus bulgaricus (L. bulgaricus) was developed using gradual increase in temperature to induce Adaptive Laboratory Evolution (ALE). Viable colony count of 1.87 ± 0.98 log cfu/mL was achieved at 52 °C, using MRS agar supplemented with 2% lactose. Changes in bacteria morphology were discovered, from rod (control) to filament (52 °C) to cocci after frozen storage (−80 °C). When milk was inoculated with thermo-tolerant L. bulgaricus, lactic acid production was absent, leaving pH at 6.84 ± 0.13. This has caused weakening of the protein network, resulting in high whey separation and lower water-holding capacity (37.1 ± 0.35%) compared to the control (98.10 ± 0.60%). Significantly higher proteolytic activity was observed through free amino acids analysis by LC-MS. Arginine and methionine (237.24 ± 5.94 and 98.83 ± 1.78 µg/100 g, respectively) were found to be 115- and 275-fold higher than the control, contributing to changing the aroma similar to cheese. Further volatile analysis through SPME-GC-MS has confirmed significant increase in cheese-aroma volatiles compared to the control, with increase in diacetyl formation. Further work on DNA profiling, metabolomics and peptidomics will help to answer mechanisms behind the observed changes made in the study.

Biotechnological Importance of Torulaspora delbrueckii: From the Obscurity to the Spotlight

Torulaspora delbrueckii has attracted interest in recent years, especially due to its biotechnological potential, arising from its flavor- and aroma-enhancing properties when used in wine, beer or bread dough fermentation, as well as from its remarkable resistance to osmotic and freezing stresses. In the present review, genomic, biochemical, and phenotypic features of T. delbrueckii are described, comparing them with other species, particularly with the biotechnologically well-established yeast, Saccharomyces cerevisiae. We conclude about the aspects that make this yeast a promising biotechnological model to be exploited in a wide range of industries, particularly in wine and bakery. A phylogenetic analysis was also performed, using the core proteome of T. delbrueckii, to compare the number of homologous proteins relative to the most closely related species, understanding the phylogenetic placement of this species with robust support. Lastly, the genetic tools available for T. delbrueckii improvement are discussed, focusing on adaptive laboratorial evolution and its potential.

Identification of new ethanol-tolerant yeast strains with fermentation potential from central Patagonia

The quest for new wild yeasts has increasingly gained attention because of their potential ability to provide unique organoleptic characters to fermented beverages. In this sense, Patagonia offers a wide diversity of ethanol-tolerant yeasts and stands out as a bioprospecting alternative. This study characterized the genetic and phenotypic diversity of yeast isolates obtained from Central Chilean Patagonia and analyzed their fermentation potential under different fermentative conditions. We recovered 125 colonies from Nothofagus spp. bark samples belonging to five yeast species: Saccharomyces eubayanus, Saccharomyces uvarum, Lachancea cidri, Kregervanrija delftensis, and Hanseniaspora valbyensis. High-throughput microcultivation assays demonstrated the extensive phenotypic diversity among Patagonian isolates, where Saccharomyces spp and L. cidri isolates exhibited the most outstanding fitness scores across the conditions tested. Fermentation performance assays under wine, mead, and beer conditions demonstrated the specific potential of the different species for each particular beverage. Saccharomyces spp. were the only isolates able to ferment beer wort. Interestingly, we found that L. cidri is a novel candidate species to ferment wine and mead, exceeding the fermentation capacity of a commercial strain. Unlike commercial strains, we found that L. cidri does not require nutritional supplements for efficient mead fermentation. In addition, L. cidri produces succinic and acetic acids, providing a distinct profile to the final fermented product. This work demonstrates the importance of bioprospecting efforts in Patagonia to isolate novel wild yeast strains with extraordinary biotechnological potential for the fermentation industry.

Packing a punch: understanding how flavours are produced in lager fermentations

Beer is one of the most popular beverages in the world and it has an irreplaceable place in culture. Although invented later than ale, lager beers dominate the current market. Many factors relating to the appearance (colour, clarity and foam stability) and sensory characters (flavour, taste and aroma) of beer, and other psychological determinants affect consumers' perception of the product and defines its drinkability. This review takes a wholistic approach to scrutinise flavour generation in the brewing process, focusing particularly on the contribution of the raw ingredients and the yeasts to the final flavour profiles of lager beers. In addition, we examine current developments to improve lager beer flavour profiles for the modern consumers.

How to characterize a strain? Clonal heterogeneity in industrial Saccharomyces influences both phenotypes and heterogeneity in phenotypes

Populations of microbes are constantly evolving heterogeneity that selection acts upon, yet heterogeneity is nontrivial to assess methodologically. The necessary practice of isolating single-cell colonies and thus subclone lineages for establishing, transferring, and using a strain results in single-cell bottlenecks with a generally neglected effect on the characteristics of the strain itself. Here, we present evidence that various subclone lineages for industrial yeasts sequenced for recent genomic studies show considerable differences, ranging from loss of heterozygosity to aneuploidies. Subsequently, we assessed whether phenotypic heterogeneity is also observable in industrial yeast, by individually testing subclone lineages obtained from products. Phenotyping of industrial yeast samples and their newly isolated subclones showed that single-cell bottlenecks during isolation can indeed considerably influence the observable phenotype. Next, we decoupled fitness distributions on the level of individual cells from clonal interference by plating single-cell colonies and quantifying colony area distributions. We describe and apply an approach using statistical modeling to compare the heterogeneity in phenotypes across samples and subclone lineages. One strain was further used to show how individual subclonal lineages are remarkably different not just in phenotype but also in the level of heterogeneity in phenotype. With these observations, we call attention to the fact that choosing an initial clonal lineage from an industrial yeast strain may vastly influence downstream performances and observations on karyotype, on phenotype, and also on heterogeneity.

Advanced strategies and tools to facilitate and streamline microbial adaptive laboratory evolution

Adaptive laboratory evolution (ALE) has served as a historic microbial engineering method that mimics natural selection to obtain desired microbes. The past decade has witnessed improvements in all aspects of ALE workflow, in terms of growth coupling, genotypic diversification, phenotypic selection, and genotype-phenotype mapping. The developing growth-coupling strategies facilitate ALE to a wider range of appealing traits. In vivo mutagenesis methods and multiplexed automated culture platforms open new gates to streamline its execution. Meanwhile, the application of multi-omics analyses and multiplexed genetic engineering promote efficient knowledge mining. This article provides a comprehensive and updated review of these advances, highlights newest significant applications, and discusses future improvements, aiming to provide a practical guide for implementation of novel, effective, and efficient ALE experiments.

Omics-Driven Biotechnology for Industrial Applications

Biomanufacturing is a key component of biotechnology that uses biological systems to produce bioproducts of commercial relevance, which are of great interest to the energy, material, pharmaceutical, food, and agriculture industries. Biotechnology-based approaches, such as synthetic biology and metabolic engineering are heavily reliant on "omics" driven systems biology to characterize and understand metabolic networks. Knowledge gained from systems biology experiments aid the development of synthetic biology tools and the advancement of metabolic engineering studies toward establishing robust industrial biomanufacturing platforms. In this review, we discuss recent advances in "omics" technologies, compare the pros and cons of the different "omics" technologies, and discuss the necessary requirements for carrying out multi-omics experiments. We highlight the influence of "omics" technologies on the production of biofuels and bioproducts by metabolic engineering. Finally, we discuss the application of "omics" technologies to agricultural and food biotechnology, and review the impact of "omics" on current COVID-19 research.

Wild Yeast for the Future: Exploring the Use of Wild Strains for Wine and Beer Fermentation

The continuous usage of single Saccharomyces cerevisiae strains as starter cultures in fermentation led to the domestication and propagation of highly specialized strains in fermentation, resulting in the standardization of wines and beers. In this way, hundreds of commercial strains have been developed to satisfy producers’ and consumers’ demands, including beverages with high/low ethanol content, nutrient deprivation tolerance, diverse aromatic profiles, and fast fermentations. However, studies in the last 20 years have demonstrated that the genetic and phenotypic diversity in commercial S. cerevisiae strains is low. This lack of diversity limits alternative wines and beers, stressing the need to explore new genetic resources to differentiate each fermentation product. In this sense, wild strains harbor a higher than thought genetic and phenotypic diversity, representing a feasible option to generate new fermentative beverages. Numerous recent studies have identified alleles in wild strains that could favor phenotypes of interest, such as nitrogen consumption, tolerance to cold or high temperatures, and the production of metabolites, such as glycerol and aroma compounds. Here, we review the recent literature on the use of commercial and wild S. cerevisiae strains in wine and beer fermentation, providing molecular evidence of the advantages of using wild strains for the generation of improved genetic stocks for the industry according to the product style.

Brewing Characteristics of the Maltotriose-Positive Yeast Zygotorulaspora florentina Isolated from Oak

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.

Developing rapid growing Bacillus subtilis for improved biochemical and recombinant protein production

Bacillus subtilis is a model Gram-positive bacterium, which has been widely used as industrially important chassis in synthetic biology and metabolic engineering. Rapid growth of chassis is beneficial for shortening the fermentation period and enhancing production of target product. However, engineered B. subtilis with faster growth phenotype is lacking. Here, fast-growing B. subtilis were constructed through rational gene knockout and adaptive laboratory evolution using wild type strain B. subtilis 168 (BS168) as starting strain. Specifically, strains BS01, BS02, and BS03 were obtained through gene knockout of oppD, hag, and flgD genes, respectively, resulting 15.37%, 24.18% and 36.46% increases of specific growth rate compared with BS168. Next, strains A28 and A40 were obtained through adaptive laboratory evolution, whose specific growth rates increased by 39.88% and 43.53% compared to BS168, respectively. Then these two methods were combined via deleting oppD, hag, and flgD genes respectively on the basis of evolved strain A40, yielding strain A4003 with further 7.76% increase of specific growth rate, reaching 0.75 h^-1 in chemical defined M9 medium. Finally, bioproduction efficiency of intracellular product (ribonucleic acid, RNA), extracellular product (acetoin), and recombinant proteins (green fluorescent protein (GFP) and ovalbumin) by fast-growing strain A4003 was tested. And the production of RNA, acetoin, GFP, and ovalbumin increased 38.09%, 5.40%, 9.47% and 19.79% using fast-growing strain A4003 as chassis compared with BS168, respectively. The developed fast-growing B. subtilis strains and strategies used for developing these strains should be useful for improving bioproduction efficiency and constructing other industrially important bacterium with faster growth phenotype.

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Fast-growing Bacillus subtilis were constructed through rational gene knockout and adaptive laboratory evolution.

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Specific growth rate of engineered B. subtilis ​increased 53.06% compared with ​B. subtilis 168, reaching 0.75 h^-1 ​in M9 medium.

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Production of RNA, acetoin, and ovalbumin increased 38.09%, 5.40%, and 19.79% using fast-growing strain as chassis.