Saccharomyces cerevisiae and its industrial applications

Exploring Core fermentation microorganisms, flavor compounds, and metabolic pathways in fermented Rice and wheat foods

The unique flavors of fermented foods significantly influence consumer purchasing choices, prompting widespread scientific interest in the flavor development process. Fermented rice and wheat foods are known for their unique flavors and they occupy an important place in the global diet. Many of these are produced on an industrial scale using starter cultures, whereas others rely on spontaneous fermentation, homemade production, or traditional activities. Microorganisms are key in shaping the sensory properties of fermented products through different metabolic pathways, thus earning the title "the essence of fermentation." Therefore, this study systematically summarizes the key microbial communities and their interactions that contribute positively to iconic fermented rice and wheat foods, such as steamed bread, bread, Mifen, and rice wine. This study revealed the mechanism by which these core microbial communities affect flavor and revealed the strategies of core microorganisms and related enzymes to enhance flavor during fermentation.

Influence of an indigenous yeast, CECA, from the Ningxia wine region of China, on the fungal and bacterial dynamics and function during Cabernet Sauvignon wine fermentation

BACKGROUND

Saccharomyces cerevisiae CECA was a potential indigenous Chinese wine yeast that can produce aroma and flavor in Cabernet Sauvignon wines. High-throughput sequencing combined with metabolite analysis was applied to analyze the effects of CECA inoculation on the native microbial community interaction and metabolism during Cabernet Sauvignon wine fermentation.

RESULTS

Fermentations were performed with three different inoculant strategies: spontaneous fermentation without inoculation, inoculation with CECA after grape must sterilization, and direct inoculation of CECA. Results showed that the diversity of bacteria (P = 0.033) is more sensitive to CECA inoculation than fungi (P = 0.563). In addition, CECA inoculation altered the species composition of core microorganisms (relative abundance >1%) and the keystone species (accounting for the top 1% of the most important interactions), as well as of the biomarkers (linear discriminant analysis > 3.0, P < 0.05). Furthermore, the inoculation could change the cluster of metabolites, and these differential metabolite sets were correlated with four fungal taxa of Issatchenkia, Issatchenkia orientalis, Saccharomycetales, Saccharomycetes and two bacterial taxa of Pantoea, Tatumella ptyseos, were significantly correlated. Inoculated fermentation also altered the correlation between dominant microorganisms and aroma compounds, giving Cabernet Sauvignon wines more herbal, floral, fruity, and cheesy aromas.

CONCLUSION

Saccharomyces cerevisiae CECA and dimethyl dicarbonate (DMDC) inhibition treatments significantly altered the microbial community structure of Cabernet Sauvignon wines, which in turn affected the microbial-metabolite correlation. These findings will help winemakers to control the microbial dynamics and functions during wine fermentation, and be more widely used in regional typical wine fermentations. © 2024 Society of Chemical Industry.

Probiotic yeast characterization and fungal amplicon metagenomics analysis of fermented bamboo shoot products from Arunachal Pradesh, northeast India

This study investigates the diverse fungal community and their probiotic functions present in ethnic fermented bamboo shoots of Arunachal Pradesh. Among 95 yeast isolates, 13 demonstrated notable probiotic attributes. These included growth at pH 3, bile tolerance, autoaggregation, co-aggregation, hydrophobicity, lysozyme tolerance and antimicrobial activity. Confirmation of some of the probiotic properties through specific primers enabled the detection of genes associated with acid and bile tolerance, antimicrobial activity, and adhesion. Probiotic yeasts were finally identified based on D1 and D2 sequences of large ribosomal subunit as Meyerozyma guilliermondii (BEP1, KGM1_3, NHR3), Meyerozyma caribbica (GEP7), Candida orthopsilopsis (ES1_2, EB1_2, EEGM2_4, GEP2, NEK9), Candida parasilopsis (HD1_1), Pichia kudriavzevii (NHR12), Pichia fermentans (BEP2), and Saccharomyces cerevisiae (NEP2). Fungal amplicon sequencing highlighted the predominance of Ascomycetes, particularly Pestalotiopsis and Penicillium genera. In this study we have perfomed a culture dependent isolation and probiotic study of yeasts and culture independent analysis of the fungal community present during the fermentation of bamboo shoots of Arunachal Pradesh which provides information about the beneficial properties of bamboo shoots as the reservoir of probiotic microorganisms.

Unveiling genetic anchors in saccharomyces cerevisiae: QTL mapping identifies IRA2 as a key player in ethanol tolerance and beyond

Ethanol stress in Saccharomyces cerevisiae is a well-studied phenomenon, but pinpointing specific genes or polymorphisms governing ethanol tolerance remains a subject of ongoing debate. Naturally found in sugar-rich environments, this yeast has evolved to withstand high ethanol concentrations, primarily produced during fermentation in the presence of suitable oxygen or sugar levels. Originally a defense mechanism against competing microorganisms, yeast-produced ethanol is now a cornerstone of brewing and bioethanol industries, where customized yeasts require high ethanol resistance for economic viability. However, yeast strains exhibit varying degrees of ethanol tolerance, ranging from 8 to 20%, making the genetic architecture of this trait complex and challenging to decipher. In this study, we introduce a novel QTL mapping pipeline to investigate the genetic markers underlying ethanol tolerance in an industrial bioethanol S. cerevisiae strain. By calculating missense mutation frequency in an allele located in a prominent QTL region within a population of 1011 S. cerevisiae strains, we uncovered rare occurrences in gene IRA2. Following molecular validation, we confirmed the significant contribution of this gene to ethanol tolerance, particularly in concentrations exceeding 12% of ethanol. IRA2 pivotal role in stress tolerance due to its participation in the Ras-cAMP pathway was further supported by its involvement in other tolerance responses, including thermotolerance, low pH tolerance, and resistance to acetic acid. Understanding the genetic basis of ethanol stress in S. cerevisiae holds promise for developing robust yeast strains tailored for industrial applications.

The Application of Fungi and Their Secondary Metabolites in Aquaculture

Ensuring sustainability has increasingly become a significant concern not only in aquaculture but in the general agrifood sector. Therefore, it is imperative to investigate pathways to feed substitutes/best practices to enhance aquaculture sustainability. The application of fungi in aquaculture provides innovative methods to enhance the sustainability and productivity of aquaculture. Fungi play numerous roles in aquaculture, including growth, immunity enhancement and disease resistance. They also play a role in bioremediation of waste and bioflocculation. The application of fungi improves the suitability and utilization of terrestrial plant ingredients in aquaculture by reducing the fibre fractions and anti-nutritional factors and increasing the nutrients and mineral contents of plant ingredients. Fungi are good flotation agents and can enhance the buoyancy of aquafeed. Pigments from fungi enhance the colouration of fish fillets, making them more attractive to consumers. This paper, via the relevant literature, explores the multifaceted roles of fungi in aquaculture, emphasizing their potential to transform aquaculture through environmentally friendly and sustainable techniques. The effectiveness of fungi in reducing fibre fractions and enhancing nutrient availability is influenced by the duration of fermentation and the dosage administered, which may differ for various feed ingredients, making it difficult for most aquaculture farmers to apply fungi approximately. Therefore, the most effective dosage and fermentation duration for each feed ingredient should be investigated.

Efficient Production of 4'-Hydroxydihydrochalcones Using Non-Conventional Yeast Strains

The quest for novel therapeutic agents has rekindled interest in natural products, particularly those derived from biotransformation processes. Dihydrochalcones, a class of plant secondary metabolites, exhibit a range of pharmacological properties. Chalcone and dihydrochalcone compounds with the characteristic 4'-hydroxy substitution are present in 'dragon's blood' resin, known for its traditional medicinal uses and complex composition, making the isolation of these compounds challenging. This study investigates the efficient production of 4'-hydroxydihydrochalcones using non-conventional yeast strains. We evaluated the biotransformation efficiency of various 4'-hydroxychalcone substrates utilizing yeast strains such as Yarrowia lipolytica KCh 71, Saccharomyces cerevisiae KCh 464, Rhodotorula rubra KCh 4 and KCh 82, and Rhodotorula glutinis KCh 242. Our findings revealed that Yarrowia lipolytica KCh 71, Rhodotorula rubra KCh 4 and KCh 82, and Rhodotorula glutinis KCh 242 exhibited the highest conversion efficiencies, exceeding 98% within one hour for most substrates. The position of methoxy substituents in the chalcone ring significantly influenced hydrogenation efficiency. Moreover, we observed isomerization of trans-4'-hydroxy-2-methoxychalcone to its cis isomer, catalyzed by light exposure. This study underscores the potential of using yeast strains for the sustainable and efficient production of dihydrochalcones, providing a foundation for developing new therapeutic agents and nutraceuticals.

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome

Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.

Mycoviruses from Aspergillus fungi involved in fermentation of dried bonito

Fungi are exploited for fermentation of foods such as cheese, Japanese sake, and soy sauce. However, the diversity of viruses that infect fungi involved in food fermentation is poorly understood. Fermented dried bonito ("katsuobushi") is one of the most important processed marine products in Japan. Fungi involved in katsuobushi fermentation are called katsuobushi molds, and Aspergillus spp. have been reported to be dominant on the surface of katsuobushi during fermentation. Because various mycoviruses have been found in members of the genus Aspergillus, we hypothesized that katsuobushi molds are also infected with mycoviruses. Here, we describe seven novel mycoviruses belonging to six families (Chrysoviridae, Fusariviridae, Mitoviridae, Partitiviridae, Polymycoviridae, and Pseudototiviridae) from isolated katsuobushi molds (Aspergillus chevalieri and A. sulphureus) detected by fragmented and primer-ligated double-stranded RNA sequencing. Aspergillus chevalieri fusarivirus 1 has a unique bi-segmented genome, whereas other known fusariviruses have a single genomic segment. Phenotypic comparison between the parental A. chevalieri strain infected with Aspergillus chevalieri polymycovirus 1 (AchPmV1) and isogenic AchPmV1-free isolates indicated that AchPmV1 inhibits the early growth of the host. This study reveals the diversity of mycoviruses that infect katsuobushi molds, and provides insight into the effect of mycoviruses on fungi involved in fermentation.

Non-Invasive Characterization of Different Saccharomyces Suspensions with Ultrasound

In fermentation processes, changes in yeast cell count and substrate concentration are indicators of yeast performance. Therefore, monitoring the composition of the biological suspension, particularly the dispersed solid phase (i.e., yeast cells) and the continuous liquid phase (i.e., medium), is a prerequisite to ensure favorable process conditions. However, the available monitoring methods are often invasive or restricted by detection limits, sampling requirements, or susceptibility to masking effects from interfering signals. In contrast, ultrasound measurements are non-invasive and provide real-time data. In this study, the suitability to characterize the dispersed and the liquid phase of yeast suspensions with ultrasound was investigated. The ultrasound signals collected from three commercially available Saccharomyces yeast were evaluated and compared. For all three yeasts, the attenuation coefficient and speed of sound increased linearly with increasing yeast concentrations (0.0-1.0 wt%) and cell counts (R2 > 0.95). Further characterization of the dispersed phase revealed that cell diameter and volume density influence the attenuation of the ultrasound signal, whereas changes in the speed of sound were partially attributed to compositional variations in the liquid phase. This demonstrates the ability of ultrasound to monitor industrial fermentations and the feasibility of developing targeted control strategies.

Naringenin and caffeic acid increase ethanol production in yeast cells by reducing very high gravity fermentation-related oxidative stress

Very high gravity (VHG) fermentation is an industrial-scale process utilizing a sugar concentration above 250 g/L to attain a significant ethanol concentration, with the advantages of decreased labor, production costs, water usage, bacterial contamination, and energy consumption. Saccharomyces cerevisiae is one of the most extensively employed organisms in ethanol fermentation through VHG technology. Conversely, high glucose exposure leads to numerous stress factors that negatively impact the ethanol production efficiency of this organism. Here, the impact of various phytochemicals added to the VHG medium on viability, glucose consumption, ethanol production efficiency, total antioxidant-oxidant status (TAS and TOS), and the response of the enzymatic antioxidant system of yeast were investigated. 2.0 mM naringenin and caffeic acid increased ethanol production by 2.453 ± 0.198 and 1.261 ± 0.138-fold, respectively. The glucose consumption rate exhibited a direct relationship with ethanol production in the naringenin-supplemented group. The highest TAS was determined as 0.734 ± 0.044 mmol Trolox Eq./L in the same group. Furthermore, both phytochemical compounds exhibited robust positive correlations with TAS (rnaringenin = 0.9986; rcaffeic acid = 0.9553) and TOS levels (rnaringenin = -0.9824; rcaffeic acid = -0.9791). While naringenin caused statistically significant increases in glutathione reductase (GR) and thioredoxin reductase (TrxR) activities, caffeic acid significantly increased TrxR and superoxide dismutase (SOD). Both phytochemicals seem to impact the ethanol production ability by regulating the redox status of the cells. We believe that the incorporation of particularly cost-effective antioxidants into the fermentation medium may serve as an alternative way to enhance the efficiency of bioethanol production using VHG technology.

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.

Overexpression of RuBisCO form I and II genes in Rhodopseudomonas palustris TIE-1 augments polyhydroxyalkanoate production heterotrophically and autotrophically

With the rising demand for sustainable renewable resources, microorganisms capable of producing bioproducts such as bioplastics are attractive. While many bioproduction systems are well-studied in model organisms, investigating non-model organisms is essential to expand the field and utilize metabolically versatile strains. This investigation centers on Rhodopseudomonas palustris TIE-1, a purple non-sulfur bacterium capable of producing bioplastics. To increase bioplastic production, genes encoding the putative regulatory protein PhaR and the depolymerase PhaZ of the polyhydroxyalkanoate (PHA) biosynthesis pathway were deleted. Genes associated with pathways that might compete with PHA production, specifically those linked to glycogen production and nitrogen fixation, were deleted. Additionally, RuBisCO form I and II genes were integrated into TIE-1's genome by a phage integration system, developed in this study. Our results show that deletion of phaR increases PHA production when TIE-1 is grown photoheterotrophically with butyrate and ammonium chloride (NH4Cl). Mutants unable to produce glycogen or fix nitrogen show increased PHA production under photoautotrophic growth with hydrogen and NH4Cl. The most significant increase in PHA production was observed when RuBisCO form I and form I & II genes were overexpressed, five times under photoheterotrophy with butyrate, two times with hydrogen and NH4Cl, and two times under photoelectrotrophic growth with N2 . In summary, inserting copies of RuBisCO genes into the TIE-1 genome is a more effective strategy than deleting competing pathways to increase PHA production in TIE-1. The successful use of the phage integration system opens numerous opportunities for synthetic biology in TIE-1.IMPORTANCEOur planet has been burdened by pollution resulting from the extensive use of petroleum-derived plastics for the last few decades. Since the discovery of biodegradable plastic alternatives, concerted efforts have been made to enhance their bioproduction. The versatile microorganism Rhodopseudomonas palustris TIE-1 (TIE-1) stands out as a promising candidate for bioplastic synthesis, owing to its ability to use multiple electron sources, fix the greenhouse gas CO2, and use light as an energy source. Two categories of strains were meticulously designed from the TIE-1 wild-type to augment the production of polyhydroxyalkanoate (PHA), one such bioplastic produced. The first group includes mutants carrying a deletion of the phaR or phaZ genes in the PHA pathway, and those lacking potential competitive carbon and energy sinks to the PHA pathway (namely, glycogen biosynthesis and nitrogen fixation). The second group comprises TIE-1 strains that overexpress RuBisCO form I or form I & II genes inserted via a phage integration system. By studying numerous metabolic mutants and overexpression strains, we conclude that genetic modifications in the environmental microbe TIE-1 can improve PHA production. When combined with other approaches (such as reactor design, use of microbial consortia, and different feedstocks), genetic and metabolic manipulations of purple nonsulfur bacteria like TIE-1 are essential for replacing petroleum-derived plastics with biodegradable plastics like PHA.

Assessing the physiological properties of baker's yeast based on single-cell Raman spectrum technology

With rapid progress in the yeast fermentation industry, a comprehensive commercial yeast quality assessment approach integrating efficiency, accuracy, sensitivity, and cost-effectiveness is required. In this study, a new yeast quality assessment method based on single-cell Raman technology was developed and contrasted with traditional methods. The findings demonstrated significant associations (Pearson correlation coefficient of 0.933 on average) between the two methods in measuring physiological indicators, including cell viability and intracellular trehalose content, demonstrating the credibility of the Raman method compared to the traditional method. Furthermore, the sensitivity of the Raman method in viable but non-culturable cells was higher in measuring yeast cell viability (17.9 % more sensitive). According to the accurate quantitative analysis of metabolic activity level (MAL) of yeast cells, the cell vitality was accurately quantified at population and single-cell levels, offering a more comprehensive assessment of yeast fermentation performance. Overall, the single-cell Raman method integrates credibility, feasibility, accuracy, and sensitivity in yeast quality assessment, offering a new technological framework for quality assessments of live-cell yeast products.

Evaluation of probiotic efficacy of indigenous yeast strain, Saccharomyces cerevisiae Y-89 isolated from a traditional fermented beverage of West Bengal, India having protective effect against DSS-induced colitis in experimental mice

Increasing awareness regarding health promotion and disease prevention has driven inclusion of fermented foods and beverages in the daily diet. These are the enormous sources of beneficial microbes, probiotics. This study aims to isolate yeast strains having probiotic potential and effectivity against colitis. Initially, ninety-two yeast strains were isolated from Haria, an ethnic fermented beverage of West Bengal, India. Primary screening was done by their acid (pH 4) and bile salt (0.3%) tolerance ability. Four potent isolates were selected and found effective against Entamoeba histolytica, as this human pathogen is responsible to cause colitis. They were identified as Saccharomyces cerevisiae. They showed luxurious growth even at 37 oC, tolerance up to 5% of NaCl, resistance to gastric juice and high bile salt (2.0%) and oro-gastrointestinal transit tolerance. They exhibited good auto-aggregation and co-aggregation ability and strong hydrophobicity. Finally, heat map and principal component analysis revealed that strain Y-89 was the best candidate. It was further characterised and found to have significant protective effects against DSS-induced colitis in experimental mice model. It includes improvement in colon length, body weight and organ indices; reduction in disease activity index; reduction in cholesterol, LDL, SGPT, SGOT, urea and creatinine levels; improvement in HDL, ALP, total protein and albumin levels; decrease in coliform count and restoration of tissue damage. This study demonstrates that the S. cerevisiae strain Y-89 possesses remarkable probiotic traits and can be used as a potential bio-therapeutic candidate for the prevention of colitis.

Encapsulation of Saccharomyces spp. for Use as Probiotic in Food and Feed: Systematic Review and Meta-analysis

Probiotics, particularly yeasts from the genus Saccharomyces, are valuable for their health benefits and potential as antibiotic alternatives. To be effective, these microorganisms must withstand harsh environmental conditions, necessitating advanced protective technologies such as encapsulation to maintain probiotic viability during processing, storage, and passage through the digestive system. This review and meta-analysis aims to describe and compare methods and agents used for encapsulating Saccharomyces spp., examining operating conditions, yeast origins, and species. It provides an overview of the literature on the health benefits of nutritional yeast consumption. A bibliographic survey was conducted following the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) guidelines. The meta-analysis compared encapsulation methods regarding their viability after encapsulation and exposure to the gastrointestinal tract. Nineteen studies were selected after applying inclusion/exclusion criteria. Freeze drying was found to be the most efficient for cell survival, while ionic gelation was best for maintaining viability after exposure to the gastrointestinal tract. Consequently, the combination of freeze drying and ionic gelation proved most effective in maintaining high cell viability during encapsulation, storage, and consumption. Research on probiotics for human food and animal feed indicates that combining freeze drying and ionic gelation effectively protects Saccharomyces spp.; however, industrial scalability must be considered. Reports on yeast encapsulation using agro-industrial residues as encapsulants offer promising strategies for preserving potential probiotic yeasts, contributing to the environmental sustainability of industrial processes.

Exploring the Antioxidant and Anti-Inflammatory Potential of Saffron (Crocus sativus) Tepals Extract within the Circular Bioeconomy

Repurposing saffron (Crocus sativus) waste presents a sustainable strategy for generating high-value products within the bioeconomy framework. Typically, flower components are discarded after stigma harvest, resulting in significant waste-350 kg of tepals per kilogram of stigmas. This research employed a comprehensive approach, integrating bioactivity studies (in vitro and in silico) with Life Cycle Assessment (LCA) evaluations, to extract and assess bioactive compounds from C. sativus tepals sourced in Tuscany, Italy. Phytochemical characterization using UPLC-MS/MS revealed a high abundance and variety of flavonoids in the hydro-ethanolic extract (CST). The antioxidant capacity was validated through various assays, and the ability to mitigate H2O2-induced oxidative stress and enhance fermentation was demonstrated in Saccharomyces cerevisiae. This study reports that C. sativus tepals extract reduces oxidative stress and boosts ethanol fermentation in yeast, paving the way for applications in the food and biofuels sectors. Further validation in RAW 264.7 macrophages confirmed CST's significant anti-inflammatory effects, indicating its potential for pharmaceutical, cosmeceutical, and nutraceutical applications. In silico studies identified potential targets involved in antioxidant and anti-inflammatory processes, shedding light on possible interaction mechanisms with Kaempferol 3-O-sophoroside (KOS-3), the predominant compound in the extract. The integration of LCA studies highlighted the environmental benefits of this approach. Overall, this research underscores the value of using waste-derived extracts through "green" methodologies, offering a model that may provide significant advantages for further evaluations compared to traditional methodologies and supporting the circular bioeconomy.

Oral immunization against foot-and-mouth disease virus using recombinant Saccharomyces cerevisiae with the improved expression of the codon-optimized VP1 fusion protein

VP1, a major immunogenic protein of foot-and-mouth disease virus (FMDV), facilitates viral attachment and entry into host cells. VP1 possesses critical epitope sequences responsible for inducing neutralizing antibodies but its expression using Saccharomyces cerevisiae has been hampered despite evidence that the presence of VP1 does not negatively impact the yeast's biology. In this study, we fused proteins to enhance VP1 expression using S. cerevisiae. Among short P1 chimeras containing VP1 including VP3-VP1 and VP2-VP1, VP3-VP1 fusion proteins showed higher expression levels than VP2-VP1. We subsequently designed new fusion proteins, of which 20 amino acids of N-terminal VP3 fused with VP1-Co1 (referred to 20aaVP3-VP1-Co1) showed the highest expression level. Lowering the culture temperature from 30 ⁰C to 20 ⁰C further enhanced fusion protein production. The highest expression level of 20aaVP3-VP1-Co1 was estimated to be 7.7 mg/L, which is comparable to other heterologous proteins produced using our S. cerevisiae expression system. Oral administration of the cell expressing 20aaVP3-VP1-Co1 induced VP1-specific IgG and IgA responses in mice. The S. cerevisiae-expressed 20aaVP3-VP1-Co1 fusion protein induced a significant immune response to the FMDV structural epitope protein, which opens the possibility of an oral FMDV vaccine.

Effects of solid-state fermentation product of yeast supplementation on liver and intestinal health, and resistance of common carp (Cyprinus carpio) against spring viraemia carp virus

This study aimed to investigate the effects of solid-state fermentation products of yeast (SFPY) on liver and intestinal health and disease resistance of common carp (Cyprinus carpio). A total of 200 common carp with an initial average weight of 2.55 ± 0.004 g were divided into 5 groups (4 replications per group and 10 fish per replication), and were fed with one of five diets, including a control diet and 4 diets supplemented with 2‰ (Y2), 3‰ (Y3), 4‰ (Y4), or 5‰ (Y5) SFPY, respectively, for 8 weeks. Results indicated that, the addition of SFPY to the diet of common carp did not affect the growth performance or survival rate of fish (P = 0.253). Interestingly, with the addition of SFPY, the triacylglycerol (TAG) content of the liver presented a linear decreasing tendency (P = 0.004), with significantly decreased in Y4 and Y5 groups (P = 0.035) compared with control. Serum lipopolysaccharide (LPS) content and diamine oxidase (DAO) activity presented a negative linear relationship with the addition of SFPY (P = 0.015, P = 0.030), while serum lipopolysaccharide binding protein (LBP) content first decreased and then increased (P < 0.001). The total antioxidant capacity (T-AOC) in the intestine of fish increased continuously with increasing SFPY supplementation (P = 0.026), reaching the highest level in Y5 group. The villus height in all experimental groups were significantly higher than that in the control group (P < 0.001). Furthermore, compared to the control, adding 3‰ SFPY to the control diet of common carp significantly increased the relative abundance of Fusobacteria (P = 0.018) and decreased that of Proteobacteria (P = 0.039) at phylum level, and increased the relative abundance of Cetobacterium (P= 0.018) and decreased that of Shewanella (P = 0.013) at genus level. Compared with the control, the relative mRNA expression level of spring viraemia of carp virus N protein (SVCV -n) in the kidney was lower than that of the control group without significance and bottomed out in Y4 group (P = 0.138). In conclusion, dietary SFPY enhanced the SVCV resistance capacity of common carp by improving liver and intestinal health and modulating the gut microbiota. Thus, SFPY is a potential feed additive to be used in aquaculture to reduce the huge economic loss of common carp due to SVCV disease. Based on liver TAG content and intestinal villus height, the optimal addition level of SFPY was 3.02‰ and 2.72‰, respectively.

Power-to-vitamins: producing folate (vitamin B9) from renewable electric power and CO2 with a microbial protein system

We recently proposed a two-stage Power-to-Protein technology to produce microbial protein from renewable electric power and CO2. Two stages were operated in series: Clostridium ljungdahlii in Stage A to reduce CO2 with H2 into acetate, and Saccharomyces cerevisiae in Stage B to utilize O2 and produce microbial protein from acetate. Renewable energy can be used to power water electrolysis to produce H2 and O2. A drawback of Stage A was the need for continuous vitamin supplementation. In this study, by using the more robust thermophilic acetogen Thermoanaerobacter kivui instead of C. ljungdahlii, vitamin supplementation was no longer needed. Additionally, S. cerevisiae produced folate when grown with acetate as a sole carbon source, achieving a total folate concentration of 6.7 mg per 100 g biomass with an average biomass concentration of 3 g l-1. The developed Power-to-Vitamin system enables folate production from renewable power and CO2 with zero or negative net-carbon emissions.

Graph-Based Pan-Genome Reveals the Pattern of Deleterious Mutations during the Domestication of Saccharomyces cerevisiae

The "cost of domestication" hypothesis suggests that the domestication of wild species increases the number, frequency, and/or proportion of deleterious genetic variants, potentially reducing their fitness in the wild. While extensively studied in domesticated species, this phenomenon remains understudied in fungi. Here, we used Saccharomyces cerevisiae, the world's oldest domesticated fungus, as a model to investigate the genomic characteristics of deleterious variants arising from fungal domestication. Employing a graph-based pan-genome approach, we identified 1,297,761 single nucleotide polymorphisms (SNPs), 278,147 insertion/deletion events (indels; <30 bp), and 19,967 non-redundant structural variants (SVs; ≥30 bp) across 687 S. cerevisiae isolates. Comparing these variants with synonymous SNPs (sSNPs) as neutral controls, we found that the majority of the derived nonsynonymous SNPs (nSNPs), indels, and SVs were deleterious. Heterozygosity was positively correlated with the impact of deleterious SNPs, suggesting a role of genetic diversity in mitigating their effects. The domesticated isolates exhibited a higher additive burden of deleterious SNPs (dSNPs) than the wild isolates, but a lower burden of indels and SVs. Moreover, the domesticated S. cerevisiae showed reduced rates of adaptive evolution relative to the wild S. cerevisiae. In summary, deleterious variants tend to be heterozygous, which may mitigate their harmful effects, but they also constrain breeding potential. Addressing deleterious alleles and minimizing the genetic load are crucial considerations for future S. cerevisiae breeding efforts.

Using Extracted Sugars from Spoiled Date Fruits as a Sustainable Feedstock for Ethanol Production by New Yeast Isolates

This study focuses on investigating sugar recovery from spoiled date fruits (SDF) for sustainable ethanol production using newly isolated yeasts. Upon their isolation from different food products, yeast strains were identified through PCR amplification of the D1/D2 region and subsequent comparison with the GenBank database, confirming isolates KKU30, KKU32, and KKU33 as Saccharomyces cerevisiae; KKU21 as Zygosaccharomyces rouxii; and KKU35m as Meyerozyma guilliermondii. Optimization of sugar extraction from SDF pulp employed response surface methodology (RSM), varying solid loading (20-40%), temperature (20-40 °C), and extraction time (10-30 min). Linear models for sugar concentration (R1) and extraction efficiency (R2) showed relatively high R2 values, indicating a good model fit. Statistical analysis revealed significant effects of temperature and extraction time on extraction efficiency. The results of batch ethanol production from SDF extracts using mono-cultures indicated varying consumption rates of sugars, biomass production, and ethanol yields among strains. Notably, S. cerevisiae strains exhibited rapid sugar consumption and high ethanol productivity, outperforming Z. rouxii and M. guilliermondii, and they were selected for scaling up the process at fed-batch mode in a co-culture. Co-cultivation resulted in complete sugar consumption and higher ethanol yields compared to mono-cultures, whereas the ethanol titer reached 46.8 ± 0.2 g/L.

Cell factories for biosynthesis of D-glucaric acid: a fusion of static and dynamic strategies

D-glucaric acid is an important organic acid with numerous applications in therapy, food, and materials, contributing significantly to its substantial market value. The biosynthesis of D-glucaric acid (GA) from renewable sources such as glucose has garnered significant attention due to its potential for sustainable and cost-effective production. This review summarizes the current understanding of the cell factories for GA production in different chassis strains, from static to dynamic control strategies for regulating their metabolic networks. We highlight recent advances in the optimization of D-glucaric acid biosynthesis, including metabolic dynamic control, alternative feedstocks, metabolic compartments, and so on. Additionally, we compare the differences between different chassis strains and discuss the challenges that each chassis strain must overcome to achieve highly efficient GA productions. In this review, the processes of engineering a desirable cell factory for highly efficient GA production are just like an epitome of metabolic engineering of strains for chemical biosynthesis, inferring general trends for industrial chassis strain developments.

Microbiological characterization of kombucha and biocellulose film produced with black tea and cocoa bean shell infusion

The food industry is increasingly striving to produce probiotics-based food and beverages using sustainable processes. Therefore, the use of by-products in product development has been investigated by several authors. The aim of this work was to investigate the effects of cocoa bean shell infusion in the production of kombucha through microbiological and genetic characterization. Three beverage formulations were prepared, one based on black tea (KBT), one based on cocoa bean shell infusion (KCS) and one containing 50 % black tea and 50 % cocoa shell infusion (KBL). The infusions were prepared with water, filtered, and sucrose was added. They were then homogenized and a portion of finished kombucha and SCOBY (symbiotic culture of bacteria and yeast) were added. Fermentation took place for 13 days and aliquots were collected every three days for physicochemical and microbial count analyses. Samples from the last day of fermentation were sent for DNA sequencing, extraction and quantification. The results were subjected to analysis of variance and compared by using Tukey's test (p < 0.05). The results show that there was a significant decrease in pH over time in all samples, while the titratable acidity increased, indicating an acidification of the beverage due to the production of organic acids. There was an increase in lactic acid bacterial colonies in all the formulations, which have a probiotic nature and are not always found in this type of beverage. Regarding the taxonomic classification of the samples, microorganisms of the kingdoms Fungi and Bacteria, of the families Saccharomycetaceae and Acetobacteraceae, were found in KBT, KCS and KBL, but with different microbiological compositions, with different amounts of yeasts and bacteria. Therefore, the use of by-products such as cocoa bean shell in the production of kombucha can contribute to the reduction of waste in the food industry and, at the same time, accelerate fermentation increasing the presence of lactic acid bacteria when compared to black tea.

Genetic modules for α-factor pheromone controlled growth regulation of Saccharomyces cerevisiae

Saccharomyces cerevisiae is a commonly used microorganism in the biotechnological industry. For the industrial heterologous production of compounds, it is of great advantage to work with growth-controllable yeast strains. In our work, we utilized the natural pheromone system of S. cerevisiae and generated a set of different strains possessing an α-pheromone controllable growth behavior. Naturally, the α-factor pheromone is involved in communication between haploid S. cerevisiae cells. Perception of the pheromone initiates several cellular changes, enabling the cells to prepare for an upcoming mating event. We exploited this natural pheromone response system and developed two different plasmid-based modules, in which the target genes, MET15 and FAR1, are under control of the α-factor sensitive FIG1 promoter for a controlled expression in S. cerevisiae. Whereas expression of MET15 led to a growth induction, FAR1 expression inhibited growth. The utilization of low copy number or high copy number plasmids for target gene expression and different concentrations of α-factor allow a finely adjustable control of yeast growth rate.

Performance of Saccharomyces cerevisiae strains against the application of adaptive laboratory evolution strategies for butanol tolerance

Although the industrial production of butanol has been carried out for decades by bacteria of the Clostridium species, recent studies have shown the use of the yeast Saccharomyces cerevisiae as a promising alternative. While the production of n-butanol by this yeast is still very far from its tolerability (up to 2% butanol), the improvement in the tolerance can lead to an increase in butanol production. The aim of the present work was to evaluate the adaptive capacity of the laboratory strain X2180-1B and the Brazilian ethanol-producing strain CAT-1 when submitted to two strategies of adaptive laboratory Evolution (ALE) in butanol. The strains were submitted, in parallel, to ALE with successive passages or with UV irradiation, using 1% butanol as selection pressure. Despite initially showing greater tolerance to butanol, the CAT-1 strain did not show great improvements after being submitted to ALE. Already the laboratory strain X2180-1B showed an incredible increase in butanol tolerance, starting from a condition of inability to grow in 1% butanol, to the capacity to grow in this same condition. With emphasis on the X2180_n100#28 isolated colony that presented the highest maximum specific growth rate among all isolated colonies, we believe that this colony has good potential to be used as a model yeast for understanding the mechanisms that involve tolerance to alcohols and other inhibitory compounds.

The role of olive leaves and saccharomyces cerevisiae supplementation in enhancing the performance and economic feasibility of fattening lambs

Objectives were to assess the use of olive leaves (OL) to replace wheat straw, the forage source, and the supplementation of Saccharomyces cerevisiae (SC) on nutritional intake, growth performance, blood parameters, and carcass quality in lambs. A total of twenty-one newly weaned Awassi lambs, weighing an average of 19 ± 0.6 kg, were randomly distributed to three groups. These three diets were: CON: 0% OL control diet; OL diet of 25%; and OL plus 0.4 g SC/head/d (OLSC) diet of 25% of dietary dry matter (DM). The first seven days were devoted to adaptation and the next sixty days were devoted to gathering data. Daily records of nutrient intake were made. On the 49th day of data collection, four animals were randomly selected from each group and kept in individual metabolism cages (1.0 × 0.8 m) with slatted mash for eight days (four days for data collection and four days for cage adaptation) to evaluate N balance and nutrient digestibility. All lambs were slaughtered after the study to assess the quality of the meat and the carcass features. No difference in DM consumption (P > 0.05) between the treatment groups. When OL-containing diets were compared to the CON diet, the consumption of acid detergent fiber and neutral detergent fiber (NDF) was lower (P ≤ 0.0002), whereas metabolizable energy and ether extract were higher (P < 0.0001). While the OL diet was intermediate, the final BW, total gain, and average daily gain for the OLSC diet tended to be higher (P < 0.087) than the CON diet. Lambs fed the OL-containing diets had a lower (P = 0.0020) cost of growth ($US/kg) than lambs in the CON group. All other nutrient digestibilities were comparable between the treatment diets, except NDF digestibility, which was greater (P = 0.045) in the OLSC group than in the CON group. The N balance variables showed a similarity between the various diets (P > 0.05). Lambs fed the OLSC diet tended to have higher weights (P ≤ 0.098) for fasting live weight, hot carcass weight, carcass cuts weights, and cold carcass weight than lambs on the CON diet. The OLSC diet resulted in higher (P < 0.025) loin weight and intermuscular fat in comparison to the CON and OL diets. No difference (P ≥ 0.05) in the dissected tissues between diets. The longissimus dorsi muscle's dimensions and physicochemical characteristics did not alter (P > 0.05) across the treatment diets. In comparison to the CON and OL diets, the OLSC diet resulted in higher serum glucose levels (P = 0.044). Nonetheless, there were similarities (P ≥ 0.05) in various serum blood parameters between the treatment diets. In conclusion, using OL or/and supplemented SC is positively associated with nutrient intake, growth performance, some carcass parameters, and loin cut tissue, and the most effective aspect is decreasing production cost ($US/kg gain), which makes it a good solution to pass inflation feedstuff prices and cover animal needs.

Feeding a Saccharomyces cerevisiae fermentation product during a gut barrier challenge in lactating Holstein cows impacts the ruminal microbiota and metabolome

Through its influence on the gut microbiota, the feeding of Saccharomyces cerevisiae fermentation products (SCFP) has been a successful strategy to enhance the health of dairy cows during periods of physiological stresses. Although production and metabolic outcomes from feeding SCFP are well-known, its combined impacts on the ruminal microbiota and metabolome during gut barrier challenges remain unclear. To address this gap in knowledge, multiparous Holstein cows (97.1 ± 7.6 DIM [SD]; n = 8/group) fed a control diet (CON) or CON plus 19 g/d SCFP for 9 wk were subjected to a feed restriction (FR) challenge for 5 d, during which they were fed 40% of their ad libitum intake from the 7 d before FR. The DNA extracted from ruminal fluid was subjected to PacBio full-length 16S rRNA gene sequencing, real-time PCR of 12 major ruminal bacteria, and metabolomics analysis of up to 189 metabolites via GC/MS. High-quality amplicon sequence analyses were performed with the TADA (Targeted Amplicon Diversity Analysis), MicrobiomeAnalyst, PICRUSt2, and STAMP software packages, and metabolomics data were analyzed via MetaboAnalyst 5.0. Ruminal fluid metabolites from the SCFP group exhibited a greater α-diversity Chao 1 (P = 0.03) and Shannon indices (P = 0.05), and the partial least squares discriminant analysis clearly discriminated metabolite profiles between dietary groups. The abundance of CPla_4_termite_group, Candidatus Saccharimonas, Oribacterium, and Pirellula genus in cows fed SCFP was greater. In the SCFP group, concentrations of ethanolamine, 2-amino-4,6-dihydroxypyrimidine, glyoxylic acid, serine, threonine, cytosine, stearic acid, and pyrrole-2-carboxylic acid were greater in ruminal fluid. Both Fretibacterium and Succinivibrio abundances were positively correlated with metabolites across various biological processes: gamma-aminobutyric acid, galactose, butane-2,3-diol, fructose, 5-amino pentanoic acid, β-aminoisobutyric acid, ornithine, malonic acid, 3-hydroxy-3-methylbutyric acid, hexanoic acid, heptanoic acid, cadaverine, glycolic acid, β-alanine, 2-hydroxybutyric acid, methyl alanine, and alanine. In the SCFP group, compared with CON, the mean proportion of 14 predicted pathways based on metabolomics data was greater, whereas 10 predicted pathways were lower. Integrating metabolites and upregulated predicted enzymes (NADP+-dependent glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, serine: glyoxylate aminotransferase, and d-glycerate 3-kinase) indicated that the pentose phosphate pathway and photorespiration pathway were most upregulated by SCFP. Overall, SCFP during FR led to alterations in ruminal microbiota composition and key metabolic pathways. Among those, we identified a shift from the tricarboxylic acid cycle to the glyoxylate cycle, and nitrogenous base production was enhanced.

Technological and Nutritional Aspects of Bread Production: An Overview of Current Status and Future Challenges

Bakery products, especially bread, exist in many homes worldwide. One of the main reasons for its high consumption is that the main raw material is wheat, a cereal that can adapt to a wide variety of soils and climates. However, the nutritional quality of this raw material decreases during its industrial processing, decreasing the value of fibers, proteins, and minerals. Therefore, bread has become a product of high interest to increase its nutritional value. Due to the high consumption of bread, this paper provides a general description of the physicochemical and rheological changes of the dough, as well as the sensory properties of bread by incorporating alternative flours such as beans, lentils, and soy (among others). The reviewed data show that alternative flours can improve fiber, macro, and micronutrient content. The high fiber content reduces the quality of the texture of the products. However, new processing steps or cooking protocols, namely flour proportions, temperature, cooking, and fermentation time, can allow adjusting production variables and optimization to potentially overcome the decrease in sensory quality and preserve consumer acceptance.

Tuning interdomain conjugation to enable in situ population modification in yeasts

The ability to modify and control natural and engineered microbiomes is essential for biotechnology and biomedicine. Fungi are critical members of most microbiomes, yet technology for modifying the fungal members of a microbiome has lagged far behind that for bacteria. Interdomain conjugation (IDC) is a promising approach, as DNA transfer from bacterial cells to yeast enables in situ modification. While such genetic transfers have been known to naturally occur in a wide range of eukaryotes and are thought to contribute to their evolution, IDC has been understudied as a technique to control fungal or fungal-bacterial consortia. One major obstacle to the widespread use of IDC is its limited efficiency. In this work, we manipulated metabolic and physical interactions between genetically tractable Escherichia coli and Saccharomyces cerevisiae to control the incidence of IDC. We test the landscape of population interactions between the bacterial donors and yeast recipients to find that bacterial commensalism leads to maximized IDC, both in culture and in mixed colonies. We demonstrate the capacity of cell-to-cell binding via mannoproteins to assist both IDC incidence and bacterial commensalism in culture and model how these tunable controls can predictably yield a range of IDC outcomes. Furthermore, we demonstrate that these controls can be utilized to irreversibly alter a recipient yeast population, by both "rescuing" a poor-growing recipient population and collapsing a stable population via a novel IDC-mediated CRISPR/Cas9 system.IMPORTANCEFungi are important but often unaddressed members of most natural and synthetic microbial communities. This work highlights opportunities for modifying yeast microbiome populations through bacterial conjugation. While conjugation has been recognized for its capacity to deliver engineerable DNA to a range of cells, its dependence on cell contact has limited its efficiency. Here, we find "knobs" to control DNA transfer, by engineering the metabolic dependence between bacterial donors and yeast recipients and by changing their ability to physically adhere to each other. Importantly, we functionally validate these "knobs" by irreversibly altering yeast populations. We use these controls to "rescue" a failing yeast population, demonstrate the capacity of conjugated CRISPR/Cas9 to depress or collapse populations, and show that conjugation can be easily interrupted by disrupting cell-to-cell binding. These results offer building blocks toward in situ mycobiome editing, with significant implications for clinical treatments of fungal pathogens and other fungal system engineering.

ER stress-induced transcriptional response reveals tolerance genes in yeast

Saccharomyces cerevisiae is important for protein secretion studies, yet the complexities of protein synthesis and secretion under endoplasmic reticulum (ER) stress conditions remain not fully understood. ER stress, triggered by alterations in the ER protein folding environment, poses substantial challenges to cells, especially during heterologous protein production. In this study, we used RNA-seq to analyze the transcriptional responses of yeast strains to ER stress induced by reagents such as tunicamycin (Tm) or dithiothreitol (DTT). Our gene expression analysis revealed several crucial genes, such as HMO1 and BIO5, that are involved in ER-stress tolerance. Through metabolic engineering, the best engineered strain R23 with HMO1 overexpression and BIO5 deletion, showed enhanced ER stress tolerance and improved protein folding efficiency, leading to a 2.14-fold increase in α-amylase production under Tm treatment and a 2.04-fold increase in cell density under DTT treatment. Our findings contribute to the understanding of cellular responses to ER stress and provide a basis for further investigations into the mechanisms of ER stress at the cellular level.

The roles of Saccharomyces cerevisiae on the bioaccessibility of phenolic compounds

Phenolic compounds are a group of non-essential dietary compounds that are widely recognized for their beneficial health effects, primarily due to their bioactive properties. These compounds which found in a variety of plant-based foods, including fruits, vegetables, and grains are known to possess antimicrobial, antioxidant, anti-inflammatory, and anti-carcinogenic properties. However, the health effects of these compounds depend on their bioaccessibility and bioavailability. In recent years, there has been growing interest in the use of probiotics for promoting human health. Saccharomyces cerevisiae is a yeast with potential probiotic properties and beneficial health effects. Biosorption of phenolic compounds on Saccharomyces cerevisiae cell walls improves their bioaccessibility. This characteristic has also allowed the use of this yeast as a biosorbent in the biosorption process due to its low cost, safety, and easy availability. S. cerevisiae enhances the bioaccessibility of phenolic compounds as a delivery system under in vitro digestion conditions. The reason for this phenomenon is the protective effects of yeast on various phenolic compounds under digestion conditions. This article shows the role of S. cerevisiae yeast on the bioaccessibility of various phenolic compounds and contributes to our understanding of the potential impact of yeasts in human health.

Emergence of Orchestrated and Dynamic Metabolism of Saccharomyces cerevisiae

Microbial metabolism is a fundamental cellular process that involves many biochemical events and is distinguished by its emergent properties. While the molecular details of individual reactions have been increasingly elucidated, it is not well understood how these reactions are quantitatively orchestrated to produce collective cellular behaviors. Here we developed a coarse-grained, systems, and dynamic mathematical framework, which integrates metabolic reactions with signal transduction and gene regulation to dissect the emergent metabolic traits of Saccharomyces cerevisiae. Our framework mechanistically captures a set of characteristic cellular behaviors, including the Crabtree effect, diauxic shift, diauxic lag time, and differential growth under nutrient-altered environments. It also allows modular expansion for zooming in on specific pathways for detailed metabolic profiles. This study provides a systems mathematical framework for yeast metabolic behaviors, providing insights into yeast physiology and metabolic engineering.

Green synthesis of yeast cell wall-derived carbon quantum dots with multiple biological activities

Hypothesis

Yeast cell walls are a sustainable biomass source containing carbon and other elements like phosphorus. Converting cell walls into valuable nanomaterials like carbon quantum dots (CQDs) is of interest.

Experiments

Cell walls from Saccharomyces cerevisiae were hydrothermally treated in 0.5 M H2SO4 to produce CQDs. Multiple analytical techniques were utilized to confirm phosphorus-doping (P-CQDs), characterize the fluorescence properties, determine quantum yield, and evaluate the sensing, antimicrobial, photocatalytic, and antioxidant capacities.

Findings

A successful synthesis of P-CQDs was achieved with strong blue fluorescence under UV excitation, 19 % quantum yield, and excellent stability. The P-CQDs showed sensitive fluorescence quenching in response to ferric ions with a 201 nM detection limit. Antibacterial effects against Escherichia coli and Staphylococcus aureus were demonstrated. P-CQDs also exhibited dye degradation under sunlight and antioxidant activity. So, the prepared P-CQDs displayed promising multifunctional capabilities for metal ion detection, disinfection, and environmental remediation. Further research is required to fully realize and implement the multifunctional potential of P-CQDs in real-world applications.

Mitigation of oxidative stress and inflammatory factors, along with the antibrowning and antimicrobial effects of cassia seed microbial fermentation solution

Introduction

Cassia seeds, originating from the mature seeds of leguminous cassia species, possess pharmacological effects attributed to their rich composition of various active ingredients, notably anthraquinones. While current research predominantly focuses on pharmaceutical extractions, there has been limited progress in fermentation studies.

Methods

Our study aimed to enhance the content of active compounds such as anthraquinones, flavonoids, and polyphenols using microbial fermentation techniques. We specifically optimized a fermentation system through a single-factor experimental design.

Results

The antioxidant properties of the fermentation solution were validated through assays involving HaCaT cells and zebrafish. We observed effective suppression of inflammatory reactions in both RAW264.7 cells and transgenic zebrafish by the fermentation solution. Moreover, significant inhibition of tyrosinase activity and melanin production was evident in B16-F10 cells and zebrafish. Positive outcomes were also obtained in antibacterial assays and chick embryo experiments.

Discussion

These findings highlight the potential of cassia seed fermentation solution as a safe and eco-friendly material in food chemistry and biomedical sciences.

The rate of adaptive molecular evolution in wild and domesticated Saccharomyces cerevisiae populations

Through its fermentative capacities, Saccharomyces cerevisiae was central in the development of civilisation during the Neolithic period, and the yeast remains of importance in industry and biotechnology, giving rise to bona fide domesticated populations. Here, we conduct a population genomic study of domesticated and wild populations of S. cerevisiae. Using coalescent analyses, we report that the effective population size of yeast populations decreased since the divergence with S. paradoxus. We fitted models of distributions of fitness effects to infer the rate of adaptive (ω a ) and non-adaptive (ω na ) non-synonymous substitutions in protein-coding genes. We report an overall limited contribution of positive selection to S. cerevisiae protein evolution, albeit with higher rates of adaptive evolution in wild compared to domesticated populations. Our analyses revealed the signature of background selection and possibly Hill-Robertson interference, as recombination was found to be negatively correlated withω na and positively correlated withω a . However, the effect of recombination onω a was found to be labile, as it is only apparent after removing the impact of codon usage bias on the synonymous site frequency spectrum and disappears if we control for the correlation withω na , suggesting that it could be an artefact of the decreasing population size. Furthermore, the rate of adaptive non-synonymous substitutions is significantly correlated with the residue solvent exposure, a relation that cannot be explained by the population's demography. Together, our results provide a detailed characterisation of adaptive mutations in protein-coding genes across S. cerevisiae populations.

Unconventional raw materials used in beer and beer-like beverages production: Impact on metabolomics and sensory profile

Beer is the third most consumed beverage in the world, trailing only water and tea but ranking first among alcoholic beverages. In recent years, producers and researchers have shown a growing interest in brewing diversification and innovation, due to of the widespread consumption of beer. In order to create beers and beer-like products with unique and consumer-pleasing characteristics, the use of unconventional raw materials has become a subject of intensive research. The purpose of this paper is to identify, evaluate and summarize the findings of all relevant unconventional raw materials used in relevant scientific studies, as well as the effect on the metabolomics of beer and beer-like beverages.For the enhancement of beer characteristics, the production process may involve the use of an extremely diverse variety of unconventional raw materials that are not included on thelist of usual ingredients for the beer industry. However, the general trend is to use locally available ingredients as well as functional ingredients. Twoof the most studied functional characteristics involve phenolic compounds and antioxidant activity, which is why the fruit is by far the most commonly used adjunct category, as fruits are particularly important sources of polyphenols and antioxidants. Other uncommon adjuncts used in brewing includeplants, starch sources, spices or even propolis. Moreover, unconventional raw materials are used to enhance the sensory profile by create new characteristics such as new tastes and flavors, accentuation of the cooling sensation or even increasing acceptability among potential consumers, who do not appreciate traditional beers due to their specific characteristics.

Enhancing Mechanical Properties of Corn Bran Arabinoxylan Films for Sustainable Food Packaging

Arabinoxylan (AX)-based films can improve the mechanical characteristics of biodegradable materials when utilized for food packaging. However, the mechanical properties of AX films for food packaging applications require thorough investigation to establish their viability. In this study, AX was extracted from corn bran coproducts of dry-milling (DCB), wet-milling (WCB), and dried distiller's grains with solubles (DDGS) using an acid-alkali method. Packaging materials were produced using these AX extracts, each combined with laccase and sorbitol, forming the basis for three different films. These films were then modified by immersing the surface in a lipase-acetate solution. We evaluated their mechanical characteristics, including thickness, tensile properties, tear resistance, and puncture resistance. The thickness and tensile properties of the modified AX films derived from DCB and DDGS showed significant improvements (p < 0.05) compared to the unmodified AX films. In contrast, the modified AX films from WCB showed no significant changes (p > 0.05) in thickness and tensile properties compared to the unmodified WCB AX films. A significant increase in tear resistance (p < 0.05) was observed in all modified AX films after immersion in the lipase-acetate mixture. While puncture resistance was enhanced in the modified AX films, the improvement was not statistically significant (p > 0.05) compared to the unmodified films. The presence of hydroxyl (OH) and carbonyl (CO) groups on the surfaces of AX films from DCB and DDGS, modified by the lipase-acetate solution, suggests excellent biodegradability properties. The modification process positively affected the AX films, rendering them more bendable, flexible, and resistant to deformation when stretched, compared to the unmodified AX films.

Biological autoluminescence enables effective monitoring of yeast cell electroporation

The application of pulsed electric fields (PEFs) is becoming a promising tool for application in biotechnology, and the food industry. However, real-time monitoring of the efficiency of PEF treatment conditions is challenging, especially at the industrial scale and in continuous production conditions.  To overcome this challenge, we have developed a straightforward setup capable of real-time detection of yeast biological autoluminescence (BAL) during pulsing. Saccharomyces cerevisiae culture was exposed to 8 pulses of 100 µs width with electric field strength magnitude 2-7 kV cm-1. To assess the sensitivity of our method in detecting yeast electroporation, we conducted a comparison with established methods including impedance measurements, propidium iodide uptake, cell growth assay, and fluorescence microscopy. Our results demonstrate that yeast electroporation can be instantaneously monitored during pulsing, making it highly suitable for industrial applications. Furthermore, the simplicity of our setup facilitates its integration into continuous liquid flow systems. Additionally, we have established quantitative indicators based on a thorough statistical analysis of the data that can be implemented through a dedicated machine interface, providing efficiency indicators for analysis.

Investigation on screening, identification, and fermentation characteristics of Yunnan olive in the fermented liquid utilizing five strains of Saccharomyces cerevisiae

Refined indigenous Saccharomyces cerevisiae can enhance refinement, sophistication, and subtlety of fruit wines by showcasing exceptional regional characteristics. In order to identify exceptional indigenous S. cerevisiae strains from Yunnan olive, this study isolated 60 yeast strains from wild Yunnan olive fermentation mash. The five S. cerevisiae strains were subjected to morphological and molecular biological identification, followed by evaluation of their fermentation performance, ethanol production capacity, ester production capacity, H2S production capacity, killing capacity, and tolerance. Strains LJM-4, LJM-10, and LJM-26 exhibited robust tolerance to 6% ethanol volume fraction, pH 2.8, sucrose concentration of 400 g/L, SO2 concentration of 0.3 g/L, glucose concentration of 400 g/L at both 40 °C and 15 °C. Additionally, strain LJM-10 demonstrated a faster fermentation rate compared to the other strains. Among the tested S. cerevisiae strains evaluated in this study for olive wine fermentation process in Yunnan region; strain LJM-10 displayed superior abilities in terms of ester and ethanol production while exhibiting the lowest H2S production levels. These findings suggest that strain LJM-10 holds great potential as an excellent candidate for optimizing fruit wine S. cerevisiae fermentation processes in Yunnan olive fruit wine.

Protective Effect of Panax notoginseng Extract Fermented by Four Different Saccharomyces cerevisiae Strains on H2O2 Induced Oxidative Stress in Skin Fibroblasts

Purpose

To produce Panax notoginseng extract as a cosmetic ingredient through Saccharomyces cerevisiae fermentation.

Methods

We first compared the total sugar content, polysaccharide content, reducing sugar content, total phenolic content, total saponin content, DPPH free radical, ABTS free radical, hydroxyl free radical scavenging ability and ferric reducing antioxidant power (FRAP) of Panax notoginseng fermented extract (pnFE) and unfermented extract (pnWE). Their potential correlations were analyzed by Pearson's correlation analysis. Then, the oxidative stress model of H2O2-induced MSFs was used to evaluate the effects of different pnFE on MSF viability, reactive oxygen species (ROS), malondialdehyde (MDA), and the activities of catalase (CAT), glutathione peroxidase (GSH-Px) and superoxide dismutase (SOD) to explore their protective effects on MSFs subjected to H2O2-induced cellular oxidative damage. Finally, their safety and stability were evaluated by using the red blood cell (RBC) test and hen's egg test-chorioallantoic membrane (HET-CAM) assay, and changes in pH and content of soluble solids, respectively.

Results

Compared with pnWE, pnFE has more active substances and stronger antioxidant capacity. In addition, pnFE has a protective effect on H2O2-induced oxidative stress in MSFs with appropriate safety and stability.

Conclusion

PnFE has broad application prospects in the field of cosmetics.

Resistance mechanisms of Saccharomyces cerevisiae against silver nanoparticles with different sizes and coatings

To investigate the underlying resistance mechanisms of Saccharomyces cerevisiae against Ag-NPs with different particle sizes and coatings, transcriptome sequencing (RNA-seq) technology was used to characterize the transcriptomes from S. cerevisiae exposed to 20-PVP-Ag, 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag, respectively. The steroid biosynthesis was found as a general pathway for Ag-NPs stress responding, in which ERG6 and ERG3 were inhibited and ERG11, ERG25 and ERG5 were significantly up-regulated to resist the stress by supporting the later mutation and resistance and modulate drug efflux indirectly. The resistance mechanism of S. cerevisiae to 20-PVP-Ag seems different from that of 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag. Under the 20-PVP-Ag, transmembrane transporter activity, transition metal ion homeostasis and oxidative phosphorylation pathway were main resistance pathways to enhance cell transport processes. While 100-PVP-Ag, 20-CIT-Ag and 100-CIT-Ag mainly impacted RNA binding, structural constituent of ribosome and ribosome pathway which can provide more energy to maintain the number and function of protein in cells. This study reveals the differences in resistance mechanisms of S. cerevisiae to Ag-NPs with different particle sizes and coatings, and explains several main regulatory mechanisms used to respond to silver stress. It will provide theoretical basis for the study of chemical risk assessment.

Cardiotoxicity and ROS Protection Assessment of three Structure-Related N-Acylhydrazones with Potential for the Treatment of Neurodegenerative Diseases

The senescence process is associated with accumulated oxidative damage and increased metal concentration in the heart and brain. Besides, abnormal metal-protein interactions have also been linked with the development of several conditions, including Alzheimer's and Parkinson's diseases. Over the years we have described a series of structure-related compounds with different activities towards models of such diseases. In this work, we evaluated the potential of three N-acylhydrazones (INHHQ: 8-hydroxyquinoline-2-carboxaldehyde isonicotinoyl hydrazone, HPCIH: pyridine-2-carboxaldehyde isonicotinoyl hydrazone and X1INH: 1-methyl-1H-imidazole-2-carboxaldehyde isonicotinoyl hydrazone) to prevent oxidative stress in cellular models, with the dual intent of being active on this pathway and also to confirm their lack of cardiotoxicity as an important step in the drug development process, especially considering that the target population often presents cardiovascular comorbidity. The 8-hydroxyquinoline-contaning compound, INHHQ, exhibits a significant cardioprotective effect against hydrogen peroxide and a robust antioxidant activity. However, this compound is the most toxic to the studied cell models and seems to induce oxidative damage on its own. Interestingly, although not possessing a phenol group in its structure, the new-generation 1-methylimidazole derivative X1INH showed a cardioprotective tendency towards H9c2 cells, demonstrating the importance of attaining a compromise between activity and intrinsic cytotoxicity when developing a drug candidate.

Ecological competition in the oral mycobiome of Hispanic adults living in Puerto Rico associates with periodontitis

Background: Fungi are a major component of the human microbiome that only recently received attention. The imbalance of indigenous fungal communities and environmental fungi present in the oral cavity may have a role in oral dysbiosis, which could exacerbate oral inflammatory diseases. Methods: We performed a cross-sectional study and recruited 88 participants aged 21 to 49 from sexually transmitted infection clinics in Puerto Rico. A full-mouth periodontal examination following the NHANES protocol defined periodontal severity (CDC/AAP). ITS2 (fungal) genes were amplified and sequenced for mycobiota characterization of yeast and environmental fungi. Environmental outdoor spore levels were measured daily by the American Academy of Allergy Asthma and Immunology San Juan station and defined by quartiles as spore scores. Results: Our data indicate polymicrobial colonization of yeast and environmental fungi in the oral cavity. Dominant taxa associated with periodontal disease included Saccharomyces cerevisiae, Rigidoporus vinctus, and Aspergillus penicilloides, while Candida albicans were found to be ubiquitous. Fungal aerosols were found to impact the oral cavity biofilm, likely due to competition and neutralization by inhaled outdoor and indoor fungal spores. Conclusion: To our knowledge, this is the first report showcasing the ecological competition of measured outdoor environmental fungi with the human oral mycobiota.

Oxygenation influences xylose fermentation and gene expression in the yeast genera Spathaspora and Scheffersomyces

BACKGROUND

Cost-effective production of biofuels from lignocellulose requires the fermentation of D-xylose. Many yeast species within and closely related to the genera Spathaspora and Scheffersomyces (both of the order Serinales) natively assimilate and ferment xylose. Other species consume xylose inefficiently, leading to extracellular accumulation of xylitol. Xylitol excretion is thought to be due to the different cofactor requirements of the first two steps of xylose metabolism. Xylose reductase (XR) generally uses NADPH to reduce xylose to xylitol, while xylitol dehydrogenase (XDH) generally uses NAD+ to oxidize xylitol to xylulose, creating an imbalanced redox pathway. This imbalance is thought to be particularly consequential in hypoxic or anoxic environments.

RESULTS

We screened the growth of xylose-fermenting yeast species in high and moderate aeration and identified both ethanol producers and xylitol producers. Selected species were further characterized for their XR and XDH cofactor preferences by enzyme assays and gene expression patterns by RNA-Seq. Our data revealed that xylose metabolism is more redox balanced in some species, but it is strongly affected by oxygen levels. Under high aeration, most species switched from ethanol production to xylitol accumulation, despite the availability of ample oxygen to accept electrons from NADH. This switch was followed by decreases in enzyme activity and the expression of genes related to xylose metabolism, suggesting that bottlenecks in xylose fermentation are not always due to cofactor preferences. Finally, we expressed XYL genes from multiple Scheffersomyces species in a strain of Saccharomyces cerevisiae. Recombinant S. cerevisiae expressing XYL1 from Scheffersomyces xylosifermentans, which encodes an XR without a cofactor preference, showed improved anaerobic growth on xylose as the primary carbon source compared to S. cerevisiae strain expressing XYL genes from Scheffersomyces stipitis.

CONCLUSION

Collectively, our data do not support the hypothesis that xylitol accumulation occurs primarily due to differences in cofactor preferences between xylose reductase and xylitol dehydrogenase; instead, gene expression plays a major role in response to oxygen levels. We have also identified the yeast Sc. xylosifermentans as a potential source for genes that can be engineered into S. cerevisiae to improve xylose fermentation and biofuel production.

Anti-Cariogenic Effects of S. cerevisiae and S. boulardii in S. mutans-C. albicans Cross-Kingdom In Vitro Models

Despite the well-documented health benefits of the probiotic Saccharomyces, its application in oral health has not been comprehensively assessed. Dental caries is a transmissible disease initiated by acid production of cariogenic bacteria and yeast, such as Streptococcus mutans and Candida albicans, on tooth enamel and followed by subsequent enamel demineralization. Here, we investigated the effect of two Saccharomyces strains (Saccharomyces boulardii and Saccharomyces cerevisiae) on S. mutans-C. albicans cross-kingdom interactions using a cariogenic planktonic model. Viable cells, pH changes, and gene expression were measured. S. cerevisiae and S. boulardii inhibited the growth of C. albicans in dual- and multi-species conditions at 4, 6, and 20 h. Saccharomyces also inhibited C. albicans hyphal formation. Furthermore, Saccharomyces reduced the acidity of the culture medium, which usually plummeted below pH 5 when S. mutans and C. albicans were present in the model. The presence of Saccharomyces maintained the culture medium above 6 even after overnight incubation, demonstrating a protective potential against dental enamel demineralization. S. boulardii significantly down-regulated S. mutans atpD and eno gene expression. Overall, our results shed light on a new promising candidate, Saccharomyces, for dental caries prevention due to its potential to create a less cariogenic environment marked by a neutral pH and reduced growth of C. albicans.

Fermentation of Plant-Based Feeds with Lactobacillus acidophilus Improves the Survival and Intestinal Health of Juvenile Nile Tilapia (Oreochromis niloticus) Reared in a Biofloc System

This study evaluated the effect of fermentation with Lactobacillus acidophilus on the biochemical and nutritional compositions of a plant-based diet and its effects on the productive performance and intestinal health of juvenile Nile tilapia (Oreochromis niloticus) reared in a biofloc technology (BFT) system. The in vitro kinetics of feed fermentation were studied to determine the L. acidophilus growth and acidification curve through counting the colony-forming units (CFUs) mL-1 and measuring the pH. Physicochemical and bromatological analyses of the feed were also performed. Based on the microbial growth kinetics results, vegetable-based Nile tilapia feeds fermented for 6 (FPB6) and 18 (FPB18) h were evaluated for 60 days. Fermented diets were compared with a positive control diet containing fishmeal (CFM) and a negative control diet without animal protein (CPB). Fermentation with L. acidophilus increased lactic acid bacteria (LAB) count and the soluble protein concentration of the plant-based feed, as well as decreasing the pH (p < 0.05). FPB treatments improved fish survival compared with CPB (p < 0.05). Fermentation increased feed intake but worsened feed efficiency (p < 0.05). The use of fermented feeds increased the LAB count and reduced pathogenic bacteria both in the BFT system's water and in the animals' intestines (p < 0.05). Fermented plant-based feeds showed greater villi (FPB6; FPB18) and higher goblet cell (FPB6) counts relative to the non-fermented plant-based feed, which may indicate improved intestinal health. The results obtained in this study are promising and show the sustainable potential of using fermented plant-based feeds in fish feeding rather than animal protein and, in particular, fishmeal.

Engineering and evolution of the complete Reductive Glycine Pathway in Saccharomyces cerevisiae for formate and CO2 assimilation

Using captured CO2 and C1-feedstocks like formate and methanol derived from electrochemical activation of CO2 are key solutions for transforming industrial processes towards a circular carbon economy. Engineering formate and CO2-based growth in the biotechnologically relevant yeast Saccharomyces cerevisiae could boost the emergence of a formate-mediated circular bio-economy. This study adopts a growth-coupled selection scheme for modular implementation of the Reductive Glycine Pathway (RGP) and subsequent Adaptive Laboratory Evolution (ALE) to enable formate and CO2 assimilation for biomass formation in yeast. We first constructed a serine biosensor strain and then implemented the serine synthesis module of the RGP into yeast, establishing glycine and serine synthesis from formate and CO2. ALE improved the RGP-dependent growth by 8-fold. 13C-labeling experiments reveal glycine, serine, and pyruvate synthesis via the RGP, demonstrating the complete pathway activity. Further, we re-established formate and CO2-dependent growth in non-evolved biosensor strains via reverse-engineering a mutation in GDH1 identified from ALE. This mutation led to significantly more 13C-formate assimilation than in WT without any selection or overexpression of the RGP. Overall, we demonstrated the activity of the complete RGP, showing evidence for carbon transfer from formate to pyruvate coupled with CO2 assimilation.

Comprehensive metabolic profiling of Geotrichum candidum and comparison with Saccharomyces cerevisiae

Geotrichum candidum is a dimorphic yeast used in cheese processing. To our knowledge, no major metabolites have been identified to date in G. candidum except for some amino acid and fatty acid metabolites. This has limited research on the commercial use of G. candidum. In this study, we aimed to analyze temporal changes in the intra- and extra-cellular metabolites of G. candidum and Saccharomyces cerevisiae cultured in YM medium as reference. As a result of metabolite analysis, it was observed that G. candidum tends to accumulate　pentose phosphate pathway compounds, which are involved in nucleic acid synthesis, after 48 h of cultivation when compared to S. cerevisiae. In addition, G. candidum accumulated higher amounts of the antioxidant glutathione in the medium than did S. cerevisiae. In addition, G. candidum accumulated large amounts of B vitamins such as pantothenic acid and nicotinic acid in the medium. Finally, we examined the potential of G. candidum as a host for the production of useful compounds such as pantothenic acid. When cultured in medium supplemented with the pantothenic acid precursor β-alanine, G. candidum produced 12-fold higher amounts of pantothenic acid (30 μM) than that by S. cerevisiae. This study indicates that G. candidum accumulates various useful compounds that are dissimilar to those produced by S. cerevisiae. Furthermore, G. candidum has the potential to produce useful chemicals under appropriate culture conditions.

Upstream and Downstream Bioprocessing in Enzyme Technology

The development of biotransformation must integrate upstream and downstream processes. Upstream bioprocessing will influence downstream bioprocessing. It is essential to consider this because downstream processes can constitute the highest cost in bioprocessing. This review comprehensively overviews the most critical aspects of upstream and downstream bioprocessing in enzymatic biocatalysis. The main upstream processes discussed are enzyme production, enzyme immobilization methodologies, solvent selection, and statistical optimization methodologies. The main downstream processes reviewed in this work are biocatalyst recovery and product separation and purification. The correct selection and combination of upstream and downstream methodologies will allow the development of a sustainable and highly productive system.

Species identification and strain discrimination of fermentation yeasts Saccharomyces cerevisiae and Saccharomyces uvarum using Raman spectroscopy and convolutional neural networks

IMPORTANCE

The use of S. cerevisiae and S. uvarum yeast starter cultures is a common practice in the alcoholic beverage fermentation industry. As yeast strains from different or the same species have variable fermentation properties, rapid and reliable typing of yeast strains plays an important role in the final quality of the product. In this study, Raman spectroscopy combined with CNN achieved accurate identification of S. cerevisiae and S. uvarum isolates at both the species and strain levels in a rapid, non-destructive, and easy-to-operate manner. This approach can be utilized to test the identity of commercialized dry yeast products and to monitor the diversity of yeast strains during fermentation. It provides great benefits as a high-throughput screening method for agri-food and the alcoholic beverage fermentation industry. This proposed method has the potential to be a powerful tool to discriminate S. cerevisiae and S. uvarum strains in taxonomic, ecological studies and fermentation applications.