Unravelling the genomic blueprint of a reference laboratory strain of the yeast Saccharomyces cerevisiae 30 years ago opened a new era in understanding yeast biology. Since then, genomics has transformed our ability to study, adapt, improve, and tailor wine yeast strains in the laboratory and manage them in the cellar. This minireview highlights key advances in wine yeast genomics, from early whole-genome sequencing of industrial S. cerevisiae strains to the recent assembly of complex non-Saccharomyces genomes, including the wine spoilage yeast Brettanomyces bruxellensis. Comparative genomics has revealed the genetic foundations of strain specific traits critical to fermentation performance, aroma production, stress tolerance, and microbial interactions in the vineyard and winery. Beyond cataloguing gene content, integrative genomic approaches have elucidated evolutionary dynamics, domestication events, and adaptation to industrial environments. These insights underpin the rational development of novel starter cultures and biotechnological interventions, fostering consistent wine quality and diversity of sensory profiles for targeted consumer markets. Looking ahead, advances in pan-genomics and functional genomics promise to deepen our understanding of metabolic networks, gene-environment interactions, and the broader ecological context of wine fermentation. Collectively, the study of wine yeast genomics not only illuminates fundamental biological principles but also provides practical tools for innovation, including pathway engineering with synthetic enzyme fusions, and the creation of purpose-built synthetic neo-chromosomes. Excitingly, S. cerevisiae, the first eukaryote to have its genome sequenced, is now poised to become the first eukaryote with an entirely synthetic genome ̶ the Sc2.0 project ̶ heralding a bold future for yeast genomics.

The qualified presumption of safety (QPS) process was developed to provide a harmonised safety assessment approach to support EFSA Scientific Panels and Units. The QPS approach assesses the taxonomic identity, body of relevant knowledge and safety of microorganisms intentionally added to the food and feed chain. Safety concerns identified for a taxonomic unit (TU) are, where possible, reflected by ‘qualifications’ that should be assessed at the strain level by EFSA's Scientific Panels. During the period covered by this Statement, no new information warranted changes to the status of previously recommended QPS TUs. The QPS list was updated to verify the correctness of the names and the completeness of synonyms. Of the 47 microorganisms notified to EFSA between April and September 2025 (28 as feed additives, 11 as food enzymes or additives, 6 as novel foods, none as plant protection products and 2 as food contact materials), 43 were not evaluated. These latter included 9 filamentous fungi and 9 Escherichia coli (all excluded from the QPS evaluation), and 25 already present on the QPS list. One of the other four notifications, Heyndrickxia faecalis (previously known as Weizmannia faecalis ) , had been assessed recently within this 3-years QPS cycle. The remaining 3 were assessed for a possible QPS status. Microchloropsis gaditana , Bacillus thermoamylovorans (both notified for the first time) and an additional TU, Aurantiochytrium acetophilum , not evaluated previously, which was included in response to an internal request. B. thermoamylovorans cannot be granted the QPS status due to the lack of body of knowledge. A. acetophilum cannot be granted the QPS status due to a limited body of knowledge. M. gaditana can be granted the QPS status with the qualification for ‘ production purpose only ’.

The Qualified Presumption of Safety (QPS) process was developed to provide a harmonised safety assessment approach to support EFSA Scientific Panels and Units. The QPS approach assesses the taxonomic identity, body of knowledge and safety of microorganisms intentionally added to the food and feed chain. Safety concerns identified for a Taxonomic Unit (TU) are, where possible, reflected by 'qualifications' that should be assessed at the strain level by EFSA's Scientific Panels. During the period covered by this Statement, no new information warranted changes to the status of previously recommended QPS TUs. Of the 99 microorganisms notified to EFSA between October 2025 and March 2026 (47 as feed additives, 32 as food enzymes or additives, 5 as novel foods and 15 as plant protection products), 85 were not evaluated. These latter included 22 filamentous fungi, 6 Escherichia coli and 2 streptomyces (all excluded from the QPS evaluation), and 55 already present on the QPS list. Of the remaining 14 notifications, corresponding to 11 TUs, 7 were already assessed in the previous QPS 3-years cycle Bacillus thuringiensis, Ensifer adhaerens, Enterococcus lactis, Heyndrickxia faecalis, Hyphomicrobium denitrificans, Microbacterium foliorum and Papiliotrema terrestris and 4 TUs were assessed for the first time: Listeria innocua, Pseudomonas protegens, Lactococcus cremoris (new species, previously a subspecies, which was part of the QPS species Lactococcus lactis) and Companilactobacillus pabuli (new species 'split' of a previous QPS species Companilactobacillus farciminis). L. cremoris, H. faecalis and C. pabuli are recommended for the QPS list, E. adhaerens also but only for production purposes. B. thuringiensis, E. lactis, P. protegens and L. innocua are not recommended for the QPS list due to safety concerns. B. thuringiensis is excluded from further QPS assessment. M. foliorum, P. terrestris and H. denitrificans are not recommended for the QPS list due to the limited body of knowledge.

The qualified presumption of safety (QPS) process was developed to provide a harmonised safety assessment approach to support EFSA Scientific Panels and Units. The QPS approach assesses the taxonomic identity, body of relevant knowledge and safety concerns of microorganisms intentionally added to the food and feed chain. Safety concerns identified for a taxonomic unit (TU) are, where possible, reflected by ‘qualifications’ that should be assessed at the strain level by EFSA's Scientific Panels. In total, 340 notifications were received between October 2022 and September 2025, of which, 190 were of microorganisms used for the production of feed additives, 87 for the production of food enzymes, food additives and flavourings, 3 for food contact materials, 22 as Plant Protection Products (PPPs) and 38 for novel foods. Bacteriophages, previously ineligible for the QPS status, are now eligible at the species level. The QPS list has been updated in relation to the most recent taxonomic insights and the qualifications were revised and streamlined. A BIOHAZ Panel Statement on how to interpret the QPS qualification on ‘acquired antimicrobial resistance genes’ was published and revised; the qualification ‘for production purposes only’ was extended to production strains or biomass; the qualification on genetic modified microorganisms (GMMs) was also extended to production strains, biomass or active agents, when the gene of concern is removed. Since 2023, Chlamydomonas reinhardtii , Microchloropsis gaditana , Candida oleophila , Vibrio natriegens and Agrobacterium radiobacter were recommended for QPS status with the qualification for ‘ production purposes only’ . Clostridium tyrobutyricum also but with the qualification ‘absence of genetic determinants for toxin production’ . Lacticaseibacillus huelsenbergensis and Lactobacillus paragasseri (formerly included in Lactobacillus gasseri ) were also included. Bacillus sonorensis was also recommended with the qualifications ‘ absence of bacitracin production ability ’ and ‘ absence of toxigenic activity ’. Bacillus thuringiensis was not recommended for the QPS list due to safety concerns.

The qualified presumption of safety (QPS) process was developed to assess the safety of microorganisms used in food and feed chains. During the period covered by this Statement, no new information warranted changes to the status of previously recommended QPS taxonomic units. The QPS list was updated to verify the correctness of the names and the completeness of synonyms. Of the 47 microorganisms notified to EFSA between October 2024 and March 2025 (25 as feed additives, 7 as food enzymes or additives, 6 as novel foods, 8 as plant protection products and 1 as food contact materials), 41 were not evaluated. These latter included 11 filamentous fungi, 4 Escherichia coli and 1 Streptomyces spp. (all excluded from the QPS evaluation), and 25 already on the QPS list. Two of the other six notifications, Bacillus thuringiensis and Ensifer adhaerens, had been previously assessed. The remaining four were assessed for a possible QPS status. Bacillus sonorensis is recommended for the QPS list with the qualifications: 'absence of bacitracin production ability' and 'absence of toxigenic activity'. Vibrio natriegens is also recommended but for 'production purposes only'. Corynebacterium stationis is not recommended due to a limited body of knowledge on its occurrence in the food and feed chain and possible safety concerns in relation to human and animal health. Papilotrema terrestris is not recommended due to a limited body of knowledge. Furthermore, Lactobacillus paragasseri (formerly included in Lactobacillus gasseri) is recommended for the QPS list. The QPS approach can also be followed if the qualifications for QPS are met due to the removal of a gene(s) of concern, by means of genetic modification. For QPS yeasts, used as active agents (viable cells), the qualification 'for production purposes only' was added for when they are used as production strains or as biomass (non-viable cells).

Ethanol stress poses a considerable challenge for Saccharomyces cerevisiae during fermentation. Strains carrying an extra copy of chromosome III exhibit enhanced ethanol tolerance. Here, we investigated the underlying mechanisms of this tolerance, focusing on gene dosage effects and differential gene expression under ethanol stress. We compared the gene expression profiles of a strain with three copies of chromosome III and its derivative with two copies, exposed to 6% and 10% ethanol. Our analysis identified TUP1, located on chromosome III, as a key regulator of the ethanol stress response. Deleting one copy of TUP1 in the tolerant strain diminished its ethanol tolerance, suggesting that chromosome III aneuploidy in ethanol-tolerant strains enhances adaptive responses by increasing TUP1 copy number. Our findings offer insights into the genetic basis of ethanol tolerance, with potential applications for optimising industrial fermentation processes and understanding the role of aneuploidy in the domestication of industrial yeasts.

The growing demand for more aromatized and complex fermented beverages has encouraged research into non-conventional yeasts that combine bio-flavor and reproducible fermentation profiles. In this study, we explore the use of the non-conventional yeast Lachancea cidri strain CBS2950 to ferment Synthetic Wine Must in single (SWM 60 and 180 mg/L YAN) and mixed (SWM 180 mg/L YAN) fermentations with the commercial Saccharomyces cerevisiae strain EC1118. We identified that L. cidri can tolerate high ethanol concentrations (10-12 % v/v) and antimicrobial compounds commonly used in wine, such as copper sulfate and potassium metabisulphite. Interestingly, L. cidri efficiently ferments SWM, even at low nitrogen concentrations (60 mg/L YAN), generating a distinct sensory profile characterized by higher concentrations of isobutanol and ethyl ester, in contrast to that in S. cerevisiae. We analyzed the L. cidri's transcriptome after 16 h of fermentation, which remained stable when comparing 180 and 60 mg/L SWM YANs, while S. cerevisiae exhibited changes in the expression of 1,704 genes, many of them related with energy precursor metabolites, highlighting its sensitivity to low nitrogen conditions. We found that the two species could co-exist in mixed fermentation under different inoculum ratios (1:1 and 10:1) throughout the process. However, gene expression profiling revealed that L. cidri was significantly impacted by the presence of S. cerevisiae, with a more significant number of genes differentially expressed than that observed under different nitrogen conditions in single-species fermentations. The different inoculum ratios tested yielded different aroma profiles, where a higher proportion of L. cidri produced a broader range of aroma compounds. In conclusion, these results highlight the potential of L. cidri in mixed fermentations by shaping the aroma compounds in wine, offering new possibilities for fermented beverages.

Starmerella bacillaris is a non-Saccharomyces yeast associated with enological niches. We present whole-genome sequences of strains FC54 and MUT5705, previously isolated from grapes and extensively characterized for their enological traits. Given the limited genomic resources, these data provide valuable insights into the genetic diversity and heterogeneity within this species.

Yeast batch fermentation is widely used in industrial biotechnology, yet its performance is strongly influenced by temperature and nitrogen availability, which affect growth kinetics and metabolite production. The development of predictive models that accurately describe these effects is essential for automating and optimizing fermentation design, reducing trial-and-error experimentation, and improving process efficiency and product quality. However, most mathematical models focus on primary metabolism and lack a systematic approach to integrate the effects of temperature. Existing models often rely on empirical corrections with limited predictive power beyond specific experimental conditions. Furthermore, there is no unified framework for optimizing fermentation processes while accounting for the temperature-dependent metabolic responses. We addressed these gaps by developing a temperature-dependent kinetic model for nitrogen-limited batch fermentation by Saccharomyces cerevisiae. The modeling approach is based on advanced systems identification, integrating identifiability analyses (structural and practical), multi-experiment parameter estimation, and automated model selection to determine the most appropriate temperature dependencies for key metabolic processes. Validated across five industrial S. cerevisiae strains in an illustrative example related to wine fermentation, the model exhibited strong predictive performance (NRMSE <10.5%, median R2>0.95) and enabled simulation-based process optimization, including nitrogen-supplementation strategies and strain selection for improved fermentation outcomes. By providing a systematic modeling framework that accounts for temperature effects, this work bridges a critical gap in predictive modeling and advances the rational design and control of industrial fermentation processes.

Ethanol toxicity is a major challenge for Saccharomyces cerevisiae during fermentation, affecting its growth and influencing the process. This study investigated the molecular mechanisms of ethanol tolerance using transcriptomics analysis of three S. cerevisiae strains chosen due to their differing levels of resistance to ethanol described in a previous work, which linked them to differences in their membrane compositions. Transcriptomic analysis revealed distinct responses in membrane lipid synthesis genes, particularly those involved in ergosterol biosynthesis, in ethanol-tolerant strains carrying a variant of the INO2 allele. This variant, which includes V263I and H86R amino acid replacements in the Ino2p transcription factor, was exclusive to ethanol-tolerant strains. CRISPR-Cas9-mediated reversion of the variant INO2 allele to the wild-type sequence in the highly tolerant strain AJ4 resulted in decreased ethanol tolerance. Our findings demonstrate the crucial role of Ino2p in ethanol tolerance through its regulation of lipid synthesis and membrane composition, highlighting the complex interplay of transcription factors in strain-specific ethanol resistance.IMPORTANCEThis study provides critical insights into the molecular basis of ethanol tolerance in Saccharomyces cerevisiae, a key trait for improving industrial fermentation processes. By identifying specific genetic variants in the Ino2p transcription factor and their impact on ethanol resistance, we reveal potential targets for enhancing yeast strain performance in high-ethanol environments. Our findings not only contribute to the fundamental understanding of stress response mechanisms in yeast but also offer practical implications for strain engineering in the biotechnology and beverage industries. The unexpected magnitude of the Ino2p variants' effect on ethanol tolerance underscores the importance of considering strain-specific genetic backgrounds in metabolic engineering strategies.

Alcoholic fermentation is an exothermic process where temperature plays a crucial role in controlling the fermentation dynamics and the quality of the final product in wineries. Temperature regimes are typically predefined, with low-temperature isothermal programs (ranging from 12 degrees C to 18 degrees C) being employed to produce white and ros & eacute; wines. These conditions foster the development and preservation of volatile compounds, but they also result in extended fermentation durations, an increased risk of fermentation interruption, and significant energy consumption. Thus, using non-isothermal temperature programs that promote yeast growth, shorten the fermentation duration, and do not compromise product quality is a relevant strategy to use in view of limiting electricity consumption. In this study, we explored the effects of different temperature programs on fermentation kinetics, metabolite production, and volatile compound profiles across nine commercial Saccharomyces cerevisiae strains in synthetic media with varying sugar concentrations. We incorporated an intuition-driven, time-varying temperature profile (TVAR), initiating at an elevated temperature to accelerate fermentation and subsequently decreasing to enhance volatile compound production. Compared to static temperatures (12 degrees C, 18 degrees C, and 25 degrees C), the TVAR program accelerated fermentation, particularly in low-sugar media, while maintaining or improving levels of volatile compounds. We found that the TVAR program enhanced the synthesis of acetate esters, ethyl hexanoate, and ethyl acetate while reducing acetate levels. Strain-specific responses and sugar content influenced results, highlighting the multiparametric nature of fermentation control and the need for precise temperature management in industrial applications. This work provides valuable data for developing automated tools to optimize fermentation in the wine industry.

ABSTRACT During batch fermentation, a variety of compounds are synthesized, as microorganisms undergo distinct growth phases: lag, exponential, growth-no-growth transition, stationary, and decay. A detailed understanding of the metabolic pathways involved in these phases is crucial for optimizing the production of target compounds. Dynamic flux balance analysis (dFBA) offers insight into the dynamics of metabolic pathways. However, explaining secondary metabolism remains a challenge. A multiphase and multi-objective dFBA scheme (MPMO model) has been proposed for this purpose. However, its formulation is discontinuous, changing from phase to phase; its accuracy in predicting intracellular fluxes is hampered by the lack of a mechanistic link between phases; and its simulation requires considerable computational effort. To address these limitations, we combine a novel model with a genome-scale model to predict the distribution of intracellular fluxes throughout batch fermentation. This integrated multiphase continuous model (IMC) has a unique formulation over time, and it incorporates empirical regulatory descriptions to automatically identify phase transitions and incorporates the hypotheses that yeasts might vary their cellular objective over time to adapt to the changing environment. We validated the predictive capacity of the IMC model by comparing its predictions with intracellular metabolomics data for Saccharomyces uvarum during batch fermentation. The model aligns well with the data, confirming its predictive capabilities. Notably, the IMC model accurately predicts trehalose accumulation, which was enforced in the MPMO model. We further demonstrate the generalizability of the IMC model, explaining the dynamics of primary and secondary metabolism of three Saccharomyces species. The model provides biological insights consistent with the literature and metabolomics data, establishing it as a valuable tool for exploring the dynamics of novel fermentation processes. IMPORTANCE This work presents an integrated multiphase continuous dynamic genome-scale model (IMC model) for batch fermentation, a crucial process widely used in industry to produce biofuels, enzymes, pharmaceuticals, and food products or ingredients. The IMC model integrates a continuous kinetic model with a genome-scale model to address the critical limitations of existing dynamic flux balance analysis schemes, such as the difficulty of explaining secondary metabolism, the lack of mechanistic links between growth phases, or the high computational demands. The model also introduces the hypothesis that cells adapt the FBA objective over time. The IMC improves the accuracy of intracellular flux predictions and simplifies the implementation process with a unique dFBA formulation over time. Its ability to predict both primary and secondary metabolism dynamics in different Saccharomyces species underscores its versatility and robustness. Furthermore, its alignment with empirical metabolomics data validates its predictive power, offering valuable insights into metabolic processes during batch fermentation. These advances pave the way for optimizing fermentation processes, potentially leading to more efficient production of target compounds and novel biotechnological applications.

The species Saccharomyces uvarum and Saccharomyces kudriavzevii have gained popularity in recent decades due to their interesting oenological properties. However, although it plays a crucial role in yeast fermentation performance and compound synthesis, our understanding of nitrogen metabolism in these species remains limited. Therefore, we compared how three strains of Saccharomyces cerevisiae, Saccharomyces uvarum and Saccharomyces kudriavzevii use relevant nitrogen sources by combining quantitative analysis approaches based on isotopic tracing and modelling. The model we have developed aims to facilitate the calculation and interpretation of stable isotope data for other experiments, by providing easy visualisation of the results and predicting the kinetics of isotope incorporation beyond the sampling points. The three species exhibit significant variations in their nitrogen assimilation profile. They differ in the timing of uptake of ammonium, arginine and glutamine: Saccharomyces cerevisiae prefers glutamine, Saccharomyces kudriavzevii ammonium and Saccharomyces uvarum arginine. This contributes to a different pattern of nitrogen redistribution towards proteinogenic amino acids between strains at the start of the exponential phase, which fades on entering the stationary phase. Additionally, we found that the contribution of leucine and valine to isoamyl alcohol production varies between species; also, Saccharomyces kudriavzevii activates the synthesis of volatile compounds earlier.

Transcriptomic studies have become an essential tool to understand the response of yeast to stimuli. The present work analyses the reaction of eight Saccharomyces cerevisiae strains with varying competitive abilities against a competitor (CR85, Saccharomyces kudriavzevii) in co-cultured fermentations. RNA sequencing (RNAseq) was performed at three very early time points after strains coinoculation in fermentation to delimit exactly when S. cerevisiae's response is triggered. A rapid response to its competitor, including activation of the glycolytic pathway, ribosomal metabolism, and nucleotide synthesis, is crucial for the dominance of S. cerevisiae strain in mixed fermentations. Additionaly, the study highlights the necessity of investigating individual yeast strains rather than a holistic species view, as significant variations in responses are observed among strains of the same clade.

The qualified presumption of safety (QPS) process was developed to provide a safety assessment approach for microorganisms intended for use in food or feed chains. In the period covered by this statement, no new information was found that would change the status of previously recommended QPS TUs. The TUs in the QPS list were updated based on a verification, against their respective authoritative databases, of the correctness of the names and completeness of synonyms. A new procedure has been established to ensure the TUs are kept up to date in relation to recent taxonomical insights. Of 83 microorganisms notified to EFSA between October 2023 and March 2024 (47 as feed additives, 25 as food enzymes or additives, 11 as novel foods), 75 were not evaluated because: 15 were filamentous fungi, 1 was Enterococcus faecium, 10 were Escherichia coli, 1 was a Streptomyces (all excluded from the QPS evaluation) and 48 were TUs that already have a QPS status. Two of the other eight notifications were already evaluated for a possible QPS status in the previous Panel Statement: Heyndrickxia faecalis (previously Weizmannia faecalis) and Serratia marcescens. One was notified at genus level so could not be assessed for QPS status. The other five notifications belonging to five TUs were assessed for possible QPS status. Akkermansia muciniphila and Actinomadura roseirufa were still not recommended for QPS status due to safety concerns. Rhizobium radiobacter can be recommended for QPS status with the qualification for production purposes. Microbacterium arborescens and Burkholderia stagnalis cannot be included in the QPS list due to a lack of body of knowledge for its use in the food and feed chain and for B. stagnalis also due to safety concerns. A. roseirufa and B. stagnalis have been excluded from further QPS assessment.

Nitrogen is essential for yeast metabolism and is often added to avoid slow or stuck fermentations in the wine industry. This study aimed to investigate the impact of different nitrogen supplementation strategies on the metabolism of various Saccharomyces yeast strains, with a particular focus on their fermentative performance, primary metabolite production, and aromatic profiles, including polyfunctional mercaptans (PFMs) varietal aromas. Two nitrogen supplements, organic (amino acids) and inorganic (NH4Cl), were evaluated under conditions and addition limits representative of the oenological industry, using Saccharomyces cerevisiae and interspecific hybrid strains (S. cerevisiae x S. uvarum and S. cerevisiae x S. kudriavzevii). The findings of this study indicate that the effect of nitrogen supplementation on yeast fermentation and aroma production is highly strain dependent. While inorganic nitrogen generally improved fermentation kinetics, its influence on metabolite production and aromatic profiles varied across strains. Nitrogen supplementation had minimal impact on ethanol, glycerol, acetic acid, and malic acid metabolism but significantly affected succinic and lactic acid production. Additionally, organic nitrogen supplementation was particularly effective in enhancing polyfunctional mercaptans (PFMs) in specific strains such as S. cerevisiae x S. kudriavzevii hybrid strains. In contrast, inorganic supplementation favoured the production of ethyl esters and medium chain fatty acids. Overall, the study emphasizes the significance of selecting the appropriate type of nitrogen based on the yeast strain and desired wine characteristics. This knowledge can help winemakers optimize fermentation processes to achieve specific sensory profiles, thereby enhancing the aromatic quality of their wines.

Hybridization between Saccharomyces cerevisiae and Saccharomyces eubayanus resulted in the emergence of S. pastorianus, a crucial yeast for lager fermentation. However, our understanding of hybridization success and hybrid vigor between these two species remains limited due to the scarcity of S. eubayanus parental strains. Here, we explore hybridization success and the impact of hybridization on fermentation performance and volatile compound profiles in newly formed lager hybrids. By selecting parental candidates spanning a diverse array of lineages from both species, we reveal that the Beer and PB-2 lineages exhibit high rates of hybridization success in S. cerevisiae and S. eubayanus, respectively. Polyploid hybrids were generated through a spontaneous diploid hybridization technique (rare-mating), revealing a prevalence of triploids and diploids over tetraploids. Despite the absence of heterosis in fermentative capacity, hybrids displayed phenotypic variability, notably influenced by maltotriose consumption. Interestingly, ploidy levels did not significantly correlate with fermentative capacity, although triploids exhibited greater phenotypic variability. The S. cerevisiae parental lineages primarily influenced volatile compound profiles, with significant differences in aroma production. Interestingly, hybrids emerging from the Beer S. cerevisiae parental lineages exhibited a volatile compound profile resembling the corresponding S. eubayanus parent. This pattern may result from the dominant inheritance of the S. eubayanus aroma profile, as suggested by the over-expression of genes related to alcohol metabolism and acetate synthesis in hybrids including the Beer S. cerevisiae lineage. Our findings suggest complex interactions between parental lineages and hybridization outcomes, highlighting the potential for creating yeasts with distinct brewing traits through hybridization strategies. IMPORTANCE:Our study investigates the principles of lager yeast hybridization between Saccharomyces cerevisiae and Saccharomyces eubayanus. This process gave rise to the lager yeast Saccharomyces pastorianus. By examining how these novel hybrids perform during fermentation and the aromas they produce, we uncover the genetic bases of brewing trait inheritance. We successfully generated polyploid hybrids using diverse strains and lineages from both parent species, predominantly triploids and diploids. Although these hybrids did not show improved fermentation capacity, they exhibited varied traits, especially in utilizing maltotriose, a key sugar in brewing. Remarkably, the aroma profiles of these hybrids were primarily influenced by the S. cerevisiae parent, with Beer lineage hybrids adopting aroma characteristics from their S. eubayanus parent. These insights reveal the complex genetic interactions in hybrid yeasts, opening new possibilities for crafting unique brewing yeasts with desirable traits.

Classifying a yeast strain into a recognized species is not always straightforward. Currently, the taxonomic delineation of yeast strains involves multiple approaches covering phenotypic characteristics and molecular methodologies, including genome-based analysis. The aim of this study was to evaluate the suitability of the Average Nucleotide Identity (ANI) calculation through FastANI, a tool created for bacterial species identification, for the assignment of strains to some yeast species. FastANI, the alignment of in silico-extracted D1/D2 sequences of LSU rRNA, and multiple alignments of orthologous genes (MAOG) were employed to analyze 644 assemblies from 12 yeast genera, encompassing various species, and on a dataset of hybrid Saccharomyces species. Overall, the analysis showed high consistency between results obtained with FastANI and MAOG, although, FastANI proved to be more discriminating than the other two methods applied to genomic sequences. In particular, FastANI was effective in distinguishing between strains belonging to different species, defining clear boundaries between them (cutoff: 94–96%). Our results show that FastANI is a reliable method for attributing a known yeast species to a particular strain. Moreover, although hybridization events make species discrimination more complex, it was revealed to be useful in the identification of these cases. We suggest its inclusion as a key component in a comprehensive approach to species delineation. Using this approach with a larger number of yeasts would validate it as a rapid technique to identify yeasts based on whole genome sequences.

This study aimed to investigate how parental genomes contribute to yeast hybrid metabolism using a metabolomic approach. Previous studies have explored central carbon and nitrogen metabolism in Saccharomyces species during wine fermentation, but this study analyses the metabolomes of Saccharomyces hybrids for the first time. We evaluated the oenological performance and intra- and extracellular metabolomes, and we compared the strains according to nutrient consumption and production of the main fermentative by-products. Surprisingly, no common pattern was observed for hybrid genome influence; each strain behaved differently during wine fermentation. However, this study suggests that the genome of the S. cerevisiae species may play a more relevant role in fermentative metabolism. Variations in biomass/nitrogen ratios were also noted, potentially linked to S. kudriavzevii and S. uvarum genome contributions. These results open up possibilities for further research using different "omics" approaches to comprehend better metabolic regulation in hybrid strains with genomes from different species.

The qualified presumption of safety (QPS) process was developed to provide a safety assessment approach for microorganisms intended for use in food or feed chains. The QPS approach is based on an assessment of published data for each taxonomic unit (TU), with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns identified for a TU are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this Statement, no new information was found that would change the status of previously recommended QPS TUs. Of 71 microorganisms notified to EFSA between April and September 2023 (30 as feed additives, 22 as food enzymes or additives, 7 as novel foods and 12 from plant protection products [PPP]), 61 were not evaluated because: 26 were filamentous fungi, 1 was Enterococcus faecium, 5 were Escherichia coli, 1 was a bacteriophage (all excluded from the QPS evaluation) and 28 were TUs that already have a QPS status. The other 10 notifications belonged to 9 TUs which were evaluated for a possible QPS status: Ensifer adhaerens and Heyndrickxia faecalis did not get the QPS recommendation due to the limited body of knowledge about their occurrence in the food and/or feed chains and Burkholderia ubonensis also due to its ability to generate biologically active compounds with antimicrobial activity; Klebsiella pneumoniae, Serratia marcescens and Pseudomonas putida due to safety concerns. K. pneumoniae is excluded from future QPS evaluations. Chlamydomonas reinhardtii is recommended for QPS status with the qualification 'for production purposes only'; Clostridium tyrobutyricum is recommended for QPS status with the qualification 'absence of genetic determinants for toxigenic activity'; Candida oleophila has been added as a synonym of Yarrowia lipolytica. The Panel clarifies the extension of the QPS status for genetically modified strains.