Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer

Modifying flavor profiles of Saccharomyces spp. for industrial brewing using FIND-IT, a non-GMO approach for metabolic engineering of yeast

Species of Saccharomyces genus have played an irreplaceable role in alcoholic beverage and baking industry for centuries. S. cerevisiae has also become an organism of choice for industrial production of alcohol and other valuable chemicals and a model organism shaping the rise of modern genetics and genomics in the past few decades. Today´s brewing industry faces challenges of decreasing consumption of traditional beer styles and increasing consumer demand for new styles, flavors and aromas. The number of currently used brewer's strains and their genetic diversity is yet limited and implementation of more genetic and phenotypic variation is seen as a solution to cope with the market challenges. This requires modification of current production strains or introduction of novel strains from other settings, e.g. industrial or wild habitats into the brewing industry. Due to legal regulation in many countries and negative customer perception of GMO organisms, the production of food and beverages requires non-GMO production organisms, whose development can be difficult and time-consuming. Here, we apply FIND-IT (Fast Identification of Nucleotide variants by DigITal PCR), an ultrafast genome-mining method, for isolation of novel yeast variants with varying flavor profiles. The FIND-IT method uses combination of random mutagenesis, droplet digital PCR with probes that target a specific desired mutation and a sub-isolation of the mutant clone. Such an approach allows the targeted identification and isolation of specific mutant strains with eliminated production of certain flavor and off-flavors and/or changes in the strain metabolism. We demonstrate that the technology is useful for the identification of loss-of function or gain of function mutations in unrelated industrial and wild strains differing in ploidy. Where no other phenotypic selection exists, this technology serves together with standard breeding techniques as a modern tool facilitating a modification of (brewer's) yeast strains leading to diversification of the product portfolio.

Advances in microbial production of geraniol: from metabolic engineering to potential industrial applications

Geraniol, an acyclic monoterpene alcohol, has significant potential applications in various fields, including: food, cosmetics, biofuels, and pharmaceuticals. However, the current sources of geraniol mainly include plant tissue extraction or chemical synthesis, which are unsustainable and suffer severely from high energy consumption and severe environmental problems. The process of microbial production of geraniol has recently undergone vigorous development. Particularly, the sustainable construction of recombinant Escherichia coli (13.2 g/L) and Saccharomyces cerevisiae (5.5 g/L) laid a solid foundation for the microbial production of geraniol. In this review, recent advances in the development of geraniol-producing strains, including: metabolic pathway construction, key enzyme improvement, genetic modification strategies, and cytotoxicity alleviation, are critically summarized. Furthermore, the key challenges in scaling up geraniol production and future perspectives for the development of robust geraniol-producing strains are suggested. This review provides theoretical guidance for the industrial production of geraniol using microbial cell factories.

Development of a Golden Gate Assembly-Based Genetic Toolbox for Lactiplantibacillus plantarum and Its Application for Engineering Monoterpenoid Biosynthesis

Lactiplantibacillus plantarum is a food-grade lactic acid bacterium widely used in the food and beverage industry. Recently, this probiotic organism has been applied as a biofactory for the production of pharmaceutical and food-related compounds, but existing promoters and expression vectors for the genetic engineering of L. plantarum rely on inefficient cloning strategies and are usually not well-characterized. We therefore developed a modular and standardized Golden Gate Assembly-based toolbox for the de novo assembly of shuttle vectors from Escherichia coli to L. plantarum. A collection of the most relevant genetic parts, e.g., different origins of replication and promoters, was incorporated in our toolbox and thoroughly characterized by flow cytometry and the fluorescence assay. Standardized fusion sites allow combining the genetic part freely into a plasmid in one step. This approach allows for the high-throughput assembly of numerous constructs in a standardized genetic context, thus improving the efficiency and predictability of metabolic engineering in L. plantarum. Using our toolbox, we were able to produce the aroma compounds linalool and geraniol in L. plantarum by extending its native mevalonate pathway with plant-derived monoterpenoid synthases.

Selection for robust metabolism in domesticated yeasts is driven by adaptation to Hsp90 stress

Protein folding both promotes and constrains adaptive evolution. We uncover this surprising duality in the role of the protein-folding chaperone heat shock protein 90 (Hsp90) in maintaining the integrity of yeast metabolism amid proteotoxic stressors within industrial domestication niches. Ethanol disrupts critical Hsp90-dependent metabolic pathways and exerts strong selective pressure for redundant duplications of key genes within these pathways, yielding the classical genomic signatures of beer and bread domestication. This work demonstrates a mechanism of adaptive canalization in an ecology of major economic importance and highlights Hsp90-dependent variation as an important source of phantom heritability in complex traits.

New developments in biotechnology applied to microorganisms

EFSA was requested by the European Commission (in accordance with Article 29 of Regulation (EC) No 178/2002) to provide a scientific opinion on the application of new developments in biotechnology (new genomic techniques, NGTs) to viable microorganisms and products of category 4 to be released into the environment or placed on the market as or in food and feed, and to non-viable products of category 3 to be placed on the market as or in food and feed. A horizon scanning exercise identified a variety of products containing microorganisms obtained with NGTs (NGT-Ms), falling within the remit of EFSA, that are expected to be placed on the (EU) market in the next 10 years. No novel potential hazards/risks from NGT-Ms were identified as compared to those obtained by established genomic techniques (EGTs), or by conventional mutagenesis. Due to the higher efficiency, specificity and predictability of NGTs, the hazards related to the changes in the genome are likely to be less frequent in NGT-Ms than those modified by EGTs and conventional mutagenesis. It is concluded that EFSA guidances are 'partially applicable', therefore on a case-by-case basis for specific NGT-Ms, fewer requirements may be needed. Some of the EFSA guidances are 'not sufficient' and updates are recommended. Because possible hazards relate to genotypic and phenotypic changes introduced and not to the method used for the modification, it is recommended that any new guidance should take a consistent risk assessment approach for strains/products derived from or produced with microorganisms obtained with conventional mutagenesis, EGTs or NGTs.

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.

Data-driven learning of structure augments quantitative prediction of biological responses

Multi-factor screenings are commonly used in diverse applications in medicine and bioengineering, including optimizing combination drug treatments and microbiome engineering. Despite the advances in high-throughput technologies, large-scale experiments typically remain prohibitively expensive. Here we introduce a machine learning platform, structure-augmented regression (SAR), that exploits the intrinsic structure of each biological system to learn a high-accuracy model with minimal data requirement. Under different environmental perturbations, each biological system exhibits a unique, structured phenotypic response. This structure can be learned based on limited data and once learned, can constrain subsequent quantitative predictions. We demonstrate that SAR requires significantly fewer data comparing to other existing machine-learning methods to achieve a high prediction accuracy, first on simulated data, then on experimental data of various systems and input dimensions. We then show how a learned structure can guide effective design of new experiments. Our approach has implications for predictive control of biological systems and an integration of machine learning prediction and experimental design.

Microbial synthesis of terpenoids for human nutrition - an emerging field with high business potential

Because of their complicated biosynthesis and hydrophobic nature, fermentative production of terpenoids did not play a significant role on a commercial scale until a few years ago. Driven by technological progress in metabolic engineering and process biotechnology, terpene-based food ingredients such as flavors, sweeteners, and vitamins produced by fermentation have now become viable and commercially competitive options. In recent years, several companies have developed microbial platforms for commercial terpene production. Impressive progress has been made in the fermentative production of sesquiterpenes used in flavorings. The development of sweeteners, such as steviol glycosides and mogrosides, and the production of vitamins A and E based on fermentation are also being explored. The production of monoterpenes remains challenging due to their antimicrobial effects.

Integrating microfluidics and synthetic biology: advancements and diverse applications across organisms

Synthetic biology is the design and modification of biological systems for specific functions, integrating several disciplines like engineering, genetics, and computer science. The field of synthetic biology is to understand biological processes within host organisms through the manipulation and regulation of their genetic pathways and the addition of biocontrol circuits to enhance their production capabilities. This pursuit serves to address global challenges spanning diverse domains that are difficult to tackle through conventional routes of production. Despite its impact, achieving precise, dynamic, and high-throughput manipulation of biological processes is still challenging. Microfluidics offers a solution to those challenges, enabling controlled fluid handling at the microscale, offering lower reagent consumption, faster analysis of biochemical reactions, automation, and high throughput screening. In this review, we diverge from conventional focus on automating the synthetic biology design-build-test-learn cycle, and instead, focus on microfluidic platforms and their role in advancing synthetic biology through its integration with host organisms - bacterial cells, yeast, fungi, animal cells - and cell-free systems. The review illustrates how microfluidic devices have been instrumental in understanding biological systems by showcasing microfluidics as an essential tool to create synthetic genetic circuits, pathways, and organisms within controlled environments. In conclusion, we show how microfluidics expedite synthetic biology applications across diverse domains including but not limited to personalized medicine, bioenergy, and agriculture.

Precision fermentation for improving the quality, flavor, safety, and sustainability of foods

Precision fermentation involves the rewiring of metabolic pathways in generally recognized as safe microorganisms, fermentation scale-up, and downstream processing to produce food ingredients from abundant and inexpensive substrates. Using precise genome editing of food-fermenting microorganisms, precision fermentation can also produce fermented foods with more desirable properties. These genetic tools allow for the manipulation of flavors and nutritional content in fermented foods, the economic production of functional food ingredients, and the sustainable production of otherwise-costly macronutrients. By introducing the metabolic designs, genetic modifications, and resulting products of engineered microorganisms developed through academic and industrial research, this review aims to provide insights into the potentials and challenges of precision fermentation for the economic, safe, and sustainable production of foods.

Pathway Evolution Through a Bottlenecking-Debottlenecking Strategy and Machine Learning-Aided Flux Balancing

The evolution of pathway enzymes enhances the biosynthesis of high-value chemicals, crucial for pharmaceutical, and agrochemical applications. However, unpredictable evolutionary landscapes of pathway genes often hinder successful evolution. Here, the presence of complex epistasis is identifued within the representative naringenin biosynthetic pathway enzymes, hampering straightforward directed evolution. Subsequently, a biofoundry-assisted strategy is developed for pathway bottlenecking and debottlenecking, enabling the parallel evolution of all pathway enzymes along a predictable evolutionary trajectory in six weeks. This study then utilizes a machine learning model, ProEnsemble, to further balance the pathway by optimizing the transcription of individual genes. The broad applicability of this strategy is demonstrated by constructing an Escherichia coli chassis with evolved and balanced pathway genes, resulting in 3.65 g L-1 naringenin. The optimized naringenin chassis also demonstrates enhanced production of other flavonoids. This approach can be readily adapted for any given number of enzymes in the specific metabolic pathway, paving the way for automated chassis construction in contemporary biofoundries.

Biosynthesis Progress of High-Energy-Density Liquid Fuels Derived from Terpenes

High-energy-density liquid fuels (HED fuels) are essential for volume-limited aerospace vehicles and could serve as energetic additives for conventional fuels. Terpene-derived HED biofuel is an important research field for green fuel synthesis. The direct extraction of terpenes from natural plants is environmentally unfriendly and costly. Designing efficient synthetic pathways in microorganisms to achieve high yields of terpenes shows great potential for the application of terpene-derived fuels. This review provides an overview of the current research progress of terpene-derived HED fuels, surveying terpene fuel properties and the current status of biosynthesis. Additionally, we systematically summarize the engineering strategies for biosynthesizing terpenes, including mining and engineering terpene synthases, optimizing metabolic pathways and cell-level optimization, such as the subcellular localization of terpene synthesis and adaptive evolution. This article will be helpful in providing insight into better developing terpene-derived HED fuels.

Edible mycelium bioengineered for enhanced nutritional value and sensory appeal using a modular synthetic biology toolkit

Filamentous fungi are critical in the transition to a more sustainable food system. While genetic modification of these organisms has promise for enhancing the nutritional value, sensory appeal, and scalability of fungal foods, genetic tools and demonstrated use cases for bioengineered food production by edible strains are lacking. Here, we develop a modular synthetic biology toolkit for Aspergillus oryzae, an edible fungus used in fermented foods, protein production, and meat alternatives. Our toolkit includes a CRISPR-Cas9 method for gene integration, neutral loci, and tunable promoters. We use these tools to elevate intracellular levels of the nutraceutical ergothioneine and the flavor-and color molecule heme in the edible biomass. The strain overproducing heme is red in color and is readily formulated into imitation meat patties with minimal processing. These findings highlight the promise of synthetic biology to enhance fungal foods and provide useful genetic tools for applications in food production and beyond.

De novo biosynthesis of the hops bioactive flavonoid xanthohumol in yeast

The flavonoid xanthohumol is an important flavor substance in the brewing industry that has a wide variety of bioactivities. However, its unstable structure results in its low content in beer. Microbial biosynthesis is considered a sustainable and economically viable alternative. Here, we harness the yeast Saccharomyces cerevisiae for the de novo biosynthesis of xanthohumol from glucose by balancing the three parallel biosynthetic pathways, prenyltransferase engineering, enhancing precursor supply, constructing enzyme fusion, and peroxisomal engineering. These strategies improve the production of the key xanthohumol precursor demethylxanthohumol (DMX) by 83-fold and achieve the de novo biosynthesis of xanthohumol in yeast. We also reveal that prenylation is the key limiting step in DMX biosynthesis and develop tailored metabolic regulation strategies to enhance the DMAPP availability and prenylation efficiency. Our work provides feasible approaches for systematically engineering yeast cell factories for the de novo biosynthesis of complex natural products.

Critical assessment of the endocrine potential of Linalool and Linalyl acetate: proactive testing strategy assessing estrogenic and androgenic activity of Lavender oil main components

The acyclic linear monoterpenes Linalool (Lin) and Linalyl acetate (LinAc) occur in nature as major constituents of various essential oils such as lavender oils. A potential endocrine activity of these compounds was discussed in literature including premature thelarche and prepubertal gynecomastia due to lavender product use. This study aims to follow-up on these critical findings reported by testing Lin and LinAc in several studies in line with current guidance and regulatory framework. No relevant anti-/ER and AR-mediated activity was observed in recombinant yeast cell-based screening tests and guideline reporter gene in vitro assays in mammalian cells. Findings in the screening test suggested an anti-androgenic activity, which could not be confirmed in the respective mammalian cell guideline assay. Mechanistic guideline in vivo studies (Uterotrophic and Hershberger assays) with Lin did not show significant dose related changes in estrogen or androgen sensitive organ weights and a guideline reproductive toxicity screening study did not reveal evident effects on sex steroid hormone sensitive organ weights, associated histopathological findings and altered sperm parameters. Estrous cycling and mating/fertility indices were not affected and no evident Lin-related steroid hormone dependent effects were found in the offspring. Overall, the initial concerns from literature were not confirmed. Findings in the yeast screening test were aberrant from follow-up guideline in vitro and in vivo studies, which underlines the need to apply careful interpretation of single in vitro test results to support a respective line of evidence and to establish a biologically plausible link to an adverse outcome.

Engineering yeast for the production of plant terpenoids using synthetic biology approaches

Covering: 2011-2022The low amounts of terpenoids produced in plants and the difficulty in synthesizing these complex structures have stimulated the production of terpenoid compounds in microbial hosts by metabolic engineering and synthetic biology approaches. Advances in engineering yeast for terpenoid production will be covered in this review focusing on four directions: (1) manipulation of host metabolism, (2) rewiring and reconstructing metabolic pathways, (3) engineering the catalytic activity, substrate selectivity and product specificity of biosynthetic enzymes, and (4) localizing terpenoid production via enzymatic fusions and scaffolds, or subcellular compartmentalization.

Mining natural products for advanced biofuels and sustainable bioproducts

Recently, there has been growing interest in the sustainable production of biofuels and bioproducts derived from renewable sources. Natural products, the largest and more structurally diverse group of metabolites, hold significant promise as sources for such bio-based products. However, there are two primary challenges in harnessing natural products' potential: precise mining of biosynthetic gene clusters (BGCs) that can be used as scaffolds or bioparts and their functional expression for biofuel and bioproduct manufacture. In this review, we explore recent advances in the development of bioinformatic tools for BGC mining and the manipulation of various hosts for natural product-based biofuels and bioproducts manufacture. Moreover, we discuss potential strategies for expanding the chemical diversity of biofuels and bioproducts and enhancing their overall yield.

Widespread biosynthesis of 16-carbon terpenoids in bacteria

Terpenoids are the most diverse group of specialized metabolites with numerous applications. Their biosynthesis is based on the five-carbon isoprene building block and, as a result, almost all terpenoids isolated to date are based on backbones that contain multiples of five carbon atoms. Intrigued by the discovery of an unusual bacterial terpenoid with a 16-carbon skeleton, here we investigate whether the biosynthesis of 16-carbon terpenoids is more widespread than this single example. We mine bacterial genomic information and identify potential C16 biosynthetic clusters in more than 700 sequenced genomes. We study selected clusters using a yeast synthetic biology platform and reveal that the encoded synthases produce at least 47 different noncanonical terpenoids. By thorough chemical analysis, we explain the structures of 13 C16 metabolites, most of which possess intricate highly strained bi- and tricyclic backbones. Our results unveil the existence of an extensive class of terpenoids in bacteria.

Climate-induced decline in the quality and quantity of European hops calls for immediate adaptation measures

A recent rise in the global brewery sector has increased the demand for high-quality, late summer hops. The effects of ongoing and predicted climate change on the yield and aroma of hops, however, remain largely unknown. Here, we combine meteorological measurements and model projections to assess the climate sensitivity of the yield, alpha content and cone development of European hops between 1970 and 2050 CE, when temperature increases by 1.4 °C and precipitation decreases by 24 mm. Accounting for almost 90% of all hop-growing regions, our results from Germany, the Czech Republic and Slovenia show that hop ripening started approximately 20 days earlier, production declined by almost 0.2 t/ha/year, and the alpha content decreased by circa 0.6% when comparing data before and after 1994 CE. A predicted decline in hop yield and alpha content of 4-18% and 20-31% by 2050 CE, respectively, calls for immediate adaptation measures to stabilize an ever-growing global sector.

Integrated meta-omics approaches reveal Saccharopolyspora as the core functional genus in huangjiu fermentations

Identification of the core functional microorganisms in food fermentations is necessary to understand the ecological and functional processes for making those foods. Wheat qu, which provides liquefaction and saccharifying power, and affects the flavor quality, is a key ingredient in ancient alcoholic huangjiu fermentation, while core microbiota of them still remains indistinct. In this study, metagenomics, metabolomics, microbial isolation and co-fermentation were used to investigate huangjiu. Although Aspergillus is usually regarded as core microorganism in wheat qu to initiate huangjiu fermentations, our metagenomic analysis showed that bacteria Saccharopolyspora are predominant in wheat qu and responsible for breakdown of starch and cellulose. Metabolic network and correlation analysis showed that Saccharopolyspora rectivirgula, Saccharopolyspora erythraea, and Saccharopolyspora hirsuta made the greatest contributions to huangjiu's metabolites, consisting of alcohols (phenylethanol, isoamylol and isobutanol), esters, amino acids (Pro, Arg, Glu and Ala) and organic acids (lactate, tartrate, acetate and citrate). S. hirsuta J2 isolated from wheat qu had the highest amylase, glucoamylase and protease activities. Co-fermentations of S. hirsuta J2 with S. cerevisiae HJ resulted in a higher fermentation rate and alcohol content, and huangjiu flavors were more similar to that of traditional huangjiu compared to co-fermentations of Aspergillus or Lactiplantibacillus with S. cerevisiae HJ. Genome of S. hirsuta J2 contained genes encoding biogenic amine degradation enzymes. By S. hirsuta J2 inoculation, biogenic amine content was reduced by 45%, 43% and 62% in huangjiu, sausage and soy sauce, respectively. These findings show the utility of Saccharopolyspora as a key functional organism in fermented food products.

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.

Ethanol Drives Evolution of Hsp90-Dependent Robustness by Redundancy in Yeast Domestication

Protein folding promotes and constrains adaptive evolution. We uncover this surprising duality in the role the protein-folding chaperone Hsp90 plays in mediating the interplay between proteome and the genome which acts to maintain the integrity of yeast metabolism in the face of proteotoxic stressors in anthropic niches. Of great industrial relevance, ethanol concentrations generated by fermentation in the making of beer and bread disrupt critical Hsp90-dependent nodes of metabolism and exert strong selective pressure for increased copy number of key genes encoding components of these nodes, yielding the classical genetic signatures of beer and bread domestication. This work establishes a mechanism of adaptive canalization in an ecology of major economic significance and highlights Hsp90-contingent variation as an important source of phantom heritability in complex traits.

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.

The microbial food revolution

Our current food system relies on unsustainable practices, which often fail to provide healthy diets to a growing population. Therefore, there is an urgent demand for new sustainable nutrition sources and processes. Microorganisms have gained attention as a new food source solution, due to their low carbon footprint, low reliance on land, water and seasonal variations coupled with a favourable nutritional profile. Furthermore, with the emergence and use of new tools, specifically in synthetic biology, the uses of microorganisms have expanded showing great potential to fulfil many of our dietary needs. In this review, we look at the different applications of microorganisms in food, and examine the history, state-of-the-art and potential to disrupt current foods systems. We cover both the use of microbes to produce whole foods out of their biomass and as cell factories to make highly functional and nutritional ingredients. The technical, economical, and societal limitations are also discussed together with the current and future perspectives.

Biosynthesis of monoterpenoid and sesquiterpenoid as natural flavors and fragrances

Terpenoids are a large class of plant-derived compounds, that constitute the main components of essential oils and are widely used as natural flavors and fragrances. The biosynthesis approach presents a promising alternative route in terpenoid production compared to plant extraction or chemical synthesis. In the past decade, the production of terpenoids using biotechnology has attracted broad attention from both academia and the industry. With the growing market of flavor and fragrance, the production of terpenoids directed by synthetic biology shows great potential in promoting future market prospects. Here, we reviewed the latest advances in terpenoid biosynthesis. The engineering strategies for biosynthetic terpenoids were systematically summarized from the enzyme, metabolic, and cellular dimensions. Additionally, we analyzed the key challenges from laboratory production to scalable production, such as key enzyme improvement, terpenoid toxicity, and volatility loss. To provide comprehensive technical guidance, we collected milestone examples of biosynthetic mono- and sesquiterpenoids, compared the current application status of chemical synthesis and biosynthesis in terpenoid production, and discussed the cost drivers based on the data of techno-economic assessment. It is expected to provide critical insights into developing translational research of terpenoid biomanufacturing.

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.

Impact of the genetic improvement of fermenting yeasts on the organoleptic properties of beer

The brewing industry has experienced a significant boom in recent years through the emergence of, on the one hand, craft breweries that produce beers with unique organoleptic characteristics, and, on the other hand, the brewing of a significant number of beers using hybridized or genetically modified microorganisms with the aim of improving both the brewing processes and the final products. This review covers the influence from yeast strains on the organoleptic properties of the final beers and also the main hybridization and genetic modification methods applied to such yeast strains with the aim of improving the sensory characteristics of the product obtained and/or the brewing process. Different approaches to the phenotypic modification of the yeasts used in beer brewing have arisen in recent years. These are dealt with in this work, with special emphasis on the methodology followed as well as on the effects of the same on the brewing process and/or on the final product.

Improving Saccharomyces cerevisiae acid and oxidative stress resistance using a prokaryotic gene identified by functional metagenomics

Innovations in obtaining products from lignocellulosic biomass have been largely based on the improvement of microorganisms and enzymes capable of degrading these materials. To complete the whole process, microorganisms must be able to ferment the resulting sugars and tolerate high concentrations of product, osmotic pressure, ion toxicity, temperature, toxic compounds from lignocellulose pretreatment, low pH, and oxidative stress. In this work, we engineered laboratory and industrial Saccharomyces cerevisiae strains by combining a gene (hu) recovered from a metagenomic approach with different native and synthetic promoters to obtain improved acid and oxidative stress resistance. Laboratorial strains harboring hu gene under the control of the synthetic stress responsive PCCW14v5 showed increased survival rates after 2 h exposure to pH 1.5. The hu gene was also able to significantly enhance the tolerance of the industrial strain to high concentrations of H₂O₂ when combined with PTEF1, PYGP1 or PYGP1v7 after 3 h exposure.

Biotransformations Performed by Yeasts on Aromatic Compounds Provided by Hop—A Review

The biodiversity of some Saccharomyces (S.) strains for fermentative activity and metabolic capacities is an important research area in brewing technology. Yeast metabolism can render simple beers very elaborate. In this review, we examine much research addressed to the study of how different yeast strains can influence aroma by chemically interacting with specific aromatic compounds (mainly terpenes) from the hop. These reactions are commonly referred to as biotransformations. Exploiting biotransformations to increase the product’s aroma and use less hop goes exactly in the direction of higher sustainability of the brewing process, as the hop generally represents the highest part of the raw materials cost, and its reduction allows to diminish its environmental impact.

Design of Four Small-Molecule-Inducible Systems in the Yeast Chromosome, Applied to Optimize Terpene Biosynthesis

The optimization of cellular functions often requires the balancing of gene expression, but the physical construction and screening of alternative designs are costly and time-consuming. Here, we construct a strain of Saccharomyces cerevisiae that contains a "sensor array" containing bacterial regulators that respond to four small-molecule inducers (vanillic acid, xylose, aTc, IPTG). Four promoters can be independently controlled with low background and a 40- to 5000-fold dynamic range. These systems can be used to study the impact of changing the level and timing of gene expression without requiring the construction of multiple strains. We apply this approach to the optimization of a four-gene heterologous pathway to the terpene linalool, which is a flavor and precursor to energetic materials. Using this approach, we identify bottlenecks in the metabolic pathway. This work can aid the rapid automated strain development of yeasts for the bio-manufacturing of diverse products, including chemicals, materials, fuels, and food ingredients.

Metabolic engineering for sustainability and health

Bio-based production of chemicals and materials has attracted much attention due to the urgent need to establish sustainability and enhance human health. Metabolic engineering (ME) allows purposeful modification of cellular metabolic, regulatory, and signaling networks to achieve enhanced production of desired chemicals and degradation of environmentally harmful chemicals. ME has significantly progressed over the past 30 years through further integration of the strategies of synthetic biology, systems biology, evolutionary engineering, and data science aided by artificial intelligence. Here we review the field of ME from its emergence to the current state-of-the-art, highlighting its contribution to sustainable production of chemicals, health, and the environment through representative examples. Future challenges of ME and perspectives are also discussed.

Microbial foods for improving human and planetary health

The current food production system is negatively impacting planetary and human health. A transition to a sustainable and fair food system is urgently needed. Microorganisms are likely enablers of this process, as they can produce delicious and healthy microbial foods with low environmental footprints. We review traditional and current approaches to microbial foods, such as fermented foods, microbial biomass, and food ingredients derived from microbial fermentations. We discuss how future advances in science-driven fermentation, synthetic biology, and sustainable feedstocks enable a new generation of microbial foods, potentially impacting the sustainability, resilience, and health effects of our food system.

Combinatorial biosynthesis: playing chess with the metabolism

Secondary metabolites are a group of natural products that produced by bacteria, fungi and plants. Many applications of these compounds from medicine to industry have been discovered. However, some changes in their structure and biosynthesis mechanism are necessary for their properties to be more suitable and also for their production to be profitable. The main and most useful method to achieve this goal is combinatorial biosynthesis. This technique uses the multi-unit essence of the secondary metabolites biosynthetic enzymes to make changes in their order, structure and also the organism that produces them.

Modern yeast development: finding the balance between tradition and innovation in contemporary winemaking

A key driver of quality in wines is the microbial population that undertakes fermentation of grape must. Winemakers can utilise both indigenous and purposefully inoculated yeasts to undertake alcoholic fermentation, imparting wines with aromas, flavours and palate structure and in many cases contributing to complexity and uniqueness. Importantly, having a toolbox of microbes helps winemakers make best use of the grapes they are presented with, and tackle fermentation difficulties with flexibility and efficiency. Each year the number of strains available commercially expands and more recently, includes strains of non-Saccharomyces, strains that have been improved using both classical and modern yeast technology and mixed cultures. Here we review what is available commercially, and what may be in the future, by exploring recent advances in fermentation relevant strain improvement technologies. We also report on the current use of microbes in the Australian wine industry, as reported by winemakers, as well as regulations around, and sentiment about the potential use of genetically modified organisms in the future.

A Toolkit for Precise, Multigene Control in Saccharomyces cerevisiae

Systems that allow researchers to precisely control the expression of genes are fundamental to biological research, biotechnology, and synthetic biology. However, few inducible gene expression systems exist that can enable simultaneous multigene control under common nutritionally favorable conditions in the important model organism and chassis Saccharomyces cerevisiae. Here we repurposed ligand binding domains from mammalian type I nuclear receptors to establish a family of up to five orthogonal synthetic gene expression systems in yeast. Our systems enable tight, independent, multigene control through addition of inert hormones and are capable of driving robust and rapid gene expression outputs, in some cases achieving up to 600-fold induction. As a proof of principle, we placed expression of four enzymes from the violacein biosynthetic pathway under independent expression control to selectively route pathway flux by addition of specific inducer combinations. Our results establish a modular, versatile, and potentially expandable toolkit for multidimensional control of gene expression in yeast that can be used to construct and control naturally occurring and synthetic gene networks.

The bright frontiers of microbial metabolic optogenetics

In recent years, light-responsive systems from the field of optogenetics have been applied to several areas of metabolic engineering with remarkable success. By taking advantage of light's high tunability, reversibility, and orthogonality to host endogenous processes, optogenetic systems have enabled unprecedented dynamical controls of microbial fermentations for chemical production, metabolic flux analysis, and population compositions in co-cultures. In this article, we share our opinions on the current state of this new field of metabolic optogenetics.We make the case that it will continue to impact metabolic engineering in increasingly new directions, with the potential to challenge existing paradigms for metabolic pathway and strain optimization as well as bioreactor operation.

Physicochemical and Sensory Properties of Czech Lager Beers with Increasing Original Wort Extract Values during Cold Storage

The scope of the study was the evaluation of the selected physicochemical (O₂ and CO₂ contents, bitterness, color, total polyphenol content (TPC), turbidity, foaming stability) and sensory properties of Czech lager beer with different original wort extract (OWE) values (OWE of 10.0; 11.0; 11.5; 12.0% w/w) during a cold storage period of 6 months (4 ± 2 °C). The length of the cold storage period did not influence the values of dissolved O₂ and CO₂, bitterness, color and foam stability of the samples. Contrarily, the TPC, turbidity, and sensory attributes of the samples were affected by the course of cold storage. The OWE values did not affect the development of the parameters tested. All beer samples stored until the 5th month presented “very good” sensory characteristics. Cold storage of beer is advantageous in order to maintain its freshness and sensory attributes at the highest level for the final consumer.

Harnessing bioengineered microbes as a versatile platform for space nutrition

Human enterprises through the solar system will entail long-duration voyages and habitation creating challenges in maintaining healthy diets. We discuss consolidating multiple sensory and nutritional attributes into microorganisms to develop customizable food production systems with minimal inputs, physical footprint, and waste. We envisage that a yeast collection bioengineered for one-carbon metabolism, optimal nutrition, and diverse textures, tastes, aromas, and colors could serve as a flexible food-production platform. Beyond its potential for supporting humans in space, bioengineered microbial-based food could lead to a new paradigm for Earth's food manufacturing that provides greater self-sufficiency and removes pressure from natural ecosystems.

Enhancement of linalool production in Saccharomyces cerevisiae by utilizing isopentenol utilization pathway

BACKGROUND

Linalool is a monoterpenoid, also a vital silvichemical with commercial applications in cosmetics, flavoring ingredients, and medicines. Regulation of mevalonate (MVA) pathway metabolic flux is a common strategy to engineer Saccharomyces cerevisiae for efficient linalool production. However, metabolic regulation of the MVA pathway is complex and involves competition for central carbon metabolism, resulting in limited contents of target metabolites.

RESULTS

In this study, first, a truncated linalool synthase (t26AaLS1) from Actinidia arguta was selected for the production of linalool in S. cerevisiae. To simplify the complexity of the metabolic regulation of the MVA pathway and increase the flux of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), we introduced the two-step isopentenyl utilization pathway (IUP) into S. cerevisiae, which could produce large amounts of IPP/DMAPP. Further, the S. cerevisiae IDI1 (ecoding isopentenyl diphosphate delta-isomerase) and ERG20^F96W-N127W (encoding farnesyl diphosphate synthase) genes were integrated into the yeast genome, combined with the strategies of copy number variation of the t26AaLS1 and ERG20^F96W-N127W genes to increase the metabolic flux of the downstream IPP, as well as optimization of isoprenol and prenol concentrations, resulting in a 4.8-fold increase in the linalool titer. Eventually, under the optimization of carbon sources and Mg²⁺ addition, a maximum linalool titer of 142.88 mg/L was obtained in the two-phase extractive shake flask fermentation.

CONCLUSIONS

The results show that the efficient synthesis of linalool in S. cerevisiae could be achieved through a two-step pathway, gene expression adjustment, and optimization of culture conditions. The study may provide a valuable reference for the other monoterpenoid production in S. cerevisiae.

Microbes of traditional fermentation processes as synthetic biology chassis to tackle future food challenges

Microbial diversity is magnificent and essential to almost all life on Earth. Microbes are an essential part of every human, allowing us to utilize otherwise inaccessible resources. It is no surprise that humans started, initially unconsciously, domesticating microbes for food production: one may call this microbial domestication 1.0. Sourdough bread is just one of the miracles performed by microbial fermentation, allowing extraction of more nutrients from flour and at the same time creating a fluffy and delicious loaf. There are a broad range of products the production of which requires fermentation such as chocolate, cheese, coffee and vinegar. Eventually, with the rise of microscopy, humans became aware of microbial life. Today our knowledge and technological advances allow us to genetically engineer microbes - one may call this microbial domestication 2.0. Synthetic biology and microbial chassis adaptation allow us to tackle current and future food challenges. One of the most apparent challenges is the limited space on Earth available for agriculture and its major tolls on the environment through use of pesticides and the replacement of ecosystems with monocultures. Further challenges include transport and packaging, exacerbated by the 24/7 on-demand mentality of many customers. Synthetic biology already tackles multiple food challenges and will be able to tackle many future food challenges. In this perspective article, we highlight recent microbial synthetic biology research to address future food challenges. We further give a perspective on how synthetic biology tools may teach old microbes new tricks, and what standardized microbial domestication could look like.

The Bibliometric Landscape of Gene Editing Innovation and Regulation in the Worldwide

Gene editing (GE) has become one of the mainstream bioengineering technologies over the past two decades, mainly fueled by the rapid development of the CRISPR/Cas system since 2012. To date, plenty of articles related to the progress and applications of GE have been published globally, but the objective, quantitative and comprehensive investigations of them are relatively few. Here, 13,980 research articles and reviews published since 1999 were collected by using GE-related queries in the Web of Science. We used bibliometric analysis to investigate the competitiveness and cooperation of leading countries, influential affiliations, and prolific authors. Text clustering methods were used to assess technical trends and research hotspots dynamically. The global application status and regulatory framework were also summarized. This analysis illustrates the bottleneck of the GE innovation and provides insights into the future trajectory of development and application of the technology in various fields, which will be helpful for the popularization of gene editing technology.

Fruits of their labour: biotransformation reactions of yeasts during brewery fermentation

Abstract

There is a growing appreciation for the role that yeast play in biotransformation of flavour compounds during beverage fermentations. This is particularly the case for brewing due to the continued popularity of aromatic beers produced via the dry-hopping process. Here, we review the current literature pertaining to biotransformation reactions mediated by fermentative yeasts. These reactions are diverse and include the liberation of thiols from cysteine or glutathione-bound adducts, as well as the release of glycosidically bound terpene alcohols. These changes serve generally to increase the fruit and floral aromas in beverages. This is particularly the case for the thiol compounds released via yeast β-lyase activity due to their low flavour thresholds. The role of yeast β-glucosidases in increasing terpene alcohols is less clear, at least with respect to fermentation of brewer’s wort. Yeast acetyl transferase and acetate esterase also have an impact on the quality and perceptibility of flavour compounds. Isomerization and reduction reactions, e.g. the conversion of geraniol (rose) to β-citronellol (citrus), also have potential to alter significantly flavour profiles. A greater understanding of biotransformation reactions is expected to not only facilitate greater control of beverage flavour profiles, but also to allow for more efficient exploitation of raw materials and thereby greater process sustainability.

Key points

• Yeast can alter and boost grape- and hop-derived flavour compounds in wine and beer

• β-lyase activity can release fruit-flavoured thiols with low flavour thresholds

• Floral and citrus-flavoured terpene alcohols can be released or interconverted

Global Metabolic Rewiring of Yeast Enables Overproduction of Sesquiterpene (+)-Valencene

(+)-Valencene is a bioactive sesquiterpene that can be used for flavoring and fragrances, and microbial production provides an alternative sustainable access. However, the complexity of cellular metabolism makes it challenging for its high-level production. Here, we report the global rewiring cellular metabolism for de novo production of (+)-valencene in yeast Saccharomyces cerevisiae by engineering central metabolism, mevalonate pathway, and sesquiterpenoid synthase. In particular, we show that metabolic transformation can help accelerate the strain construction process and multiple copy expression of sesquiterpenoid synthase is essential for boosting the metabolic flux for product synthesis with enhanced supply of precursors. The engineered strain produced 1.2 g/L (+)-valencene under fed-batch fermentation in shake flasks, which was increased by 549-fold and demonstrated great potential of the yeast cell factory for (+)-valencene production.

Maltose-Negative Yeast in Non-Alcoholic and Low-Alcoholic Beer Production

Although beer is a widely used beverage in many cultures, there is a need for a new drinking alternative in the face of rising issues such as health concerns or weight problems. However, non-alcoholic and low-alcoholic beers (NABLAB) still have some sensory problems that have not been fully remedied today, such as “wort-like”/”potato-like” flavours or a lack of aroma. These defects are due to the lack of alcohol (and the lack of the aldehyde-reducing effect of alcohol fermentation), as well as production techniques. The use of new yeast strains that cannot ferment maltose—the foremost sugar in the wort—is highly promising to produce a more palatable and sustainable NABLAB product because production with these yeast strains can be performed with standard brewery equipment. In the scientific literature, it is clear that interest in the production of NABLAB has increased recently, and experiments have been carried out with maltose-negative yeast strains isolated from many different environments. This study describes maltose-negative yeasts and their aromatic potential for the production of NABLAB by comprehensively examining recent academic studies.

Engineering Saccharomyces cerevisiae for production of the capsaicinoid nonivamide

Background

Capsaicinoids are produced by plants in the Capsicum genus and are the main reason for the pungency of chili pepper fruits. They are strong agonists of TRPV1 (the transient receptor potential cation channel subfamily V member 1) and used as active ingredients in pharmaceuticals for the treatment of pain. The use of bioengineered microorganisms in a fermentation process may be an efficient route for their preparation, as well as for the discovery of (bio-)synthetic capsaicinoids with improved or novel bioactivities.

Results

Saccharomyces cerevisiae was engineered to over-express a selection of amide-forming N-acyltransferase and CoA-ligase enzyme cascades using a combinatorial gene assembly method, and was screened for nonivamide production from supplemented vanillylamine and nonanoic acid. Data from this work demonstrate that Tyramine N-hydroxycinnamoyl transferase from Capsicum annuum (CaAT) was most efficient for nonivamide formation in yeast, outcompeting the other candidates including AT3 (Pun1) from Capsicum spp. The CoA-ligase partner with highest activity from the ones evaluated here were from Petunia hybrida (PhCL) and Spingomonas sp. Ibu-2 (IpfF). A yeast strain expressing CaAT and IpfF produced 10.6 mg L⁻¹ nonivamide in a controlled bioreactor setup, demonstrating nonivamide biosynthesis by S. cerevisiae for the first time.

Conclusions

Baker’s yeast was engineered for production of nonivamide as a model capsaicinoid, by expressing N-acyltransferases and CoA-ligases of plant and bacterial origin. The constructed yeast platform holds potential for in vivo biocatalytic formation of capsaicinoids and could be a useful tool for the discovery of novel drugs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01831-3.

Surmounting the off-flavor challenge in plant-based foods

Plant-based food products have been receiving an astronomical amount of attention recently, and their demand will most likely soar in the future. However, their unpleasant, intrinsic flavor and odor are the major obstacles limiting consumer's acceptance. These off-flavors are often described as "green," "grassy," "beany," "fatty" and "bitter." This review highlights the presence and formation of common off-flavor volatiles (aldehydes, alcohols, ketones, pyrazines, furans) and nonvolatiles (phenolics, saponins, peptides, alkaloids) from a variety of plant-based foods, including legumes (e.g. lentil, soy, pea), fruits (e.g. apple, grape, watermelon) and vegetables (e.g. carrot, potato, radish). These compounds are formed through various pathways, including lipid oxidation, ethanol fermentation and Maillard reaction (and Strecker degradation). The effect of off-flavor compounds as received by the human taste receptors, along with its possible link of bioactivity (e.g. anti-inflammatory effect), are briefly discussed on a molecular level. Generation of off-flavor compounds in plants is markedly affected by the species, cultivar, geographical location, climate conditions, farming and harvest practices. The effects of genome editing (i.e. CRISPR-Cas9), various processing technologies, such as antioxidant supplementation, enzyme treatment, extrusion, fermentation, pressure application, and different storage and packaging conditions, have been increasingly studied in recent years to mitigate the formation of off-flavors in plant foods. The information presented in this review could be useful for agricultural practitioners, fruits and vegetables industry, and meat and dairy analogue manufacturers to improve the flavor properties of plant-based foods.