Journal articles on the topic 'Novel yeast fermentation metabolite profiles'
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1
da Silva Vale, Alexander, Gabriel Balla, Luiz Roberto Saldanha Rodrigues, Dão Pedro de Carvalho Neto, Carlos Ricardo Soccol, and Gilberto Vinícius de Melo Pereira. "Understanding the Effects of Self-Induced Anaerobic Fermentation on Coffee Beans Quality: Microbiological, Metabolic, and Sensory Studies." Foods 12, no. 1 (December 22, 2022): 37. http://dx.doi.org/10.3390/foods12010037.
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In this study, an investigation of the microbial community structure and chemical changes in different layers of a static coffee beans fermentation tank (named self-induced anaerobic fermentation—SIAF) was conducted at different times (24, 48, and 72 h). The microbial taxonomic composition comprised a high prevalence of Enterobacteriaceae and Nectriaceae and low prevalence of lactic acid bacteria and yeast, which greatly differs from the traditional process performed in open tanks. No major variation in bacterial and fungal diversity was observed between the bottom, middle, and top layers of the fermentation tank. On the other hand, the metabolism of these microorganisms varied significantly, showing a higher consumption of pulp sugar and production of metabolites in the bottom and middle layers compared to the top part of the fermentation tank. Extended processes (48 and 72 h) allowed a higher production of key-metabolites during fermentation (e.g., 3-octanol, ethyl acetate, and amyl acetate), accumulation in roasted coffee beans (acetic acid, pyrazine, methyl, 2-propanone, 1-hydroxy), and diversification of sensory profiles of coffee beverages compared to 24 h of fermentation process. In summary, this study demonstrated that SIAF harbored radically different dominant microbial groups compared to traditional coffee processing, and diversification of fermentation time could be an important tool to provide coffee beverages with novel and desirable flavor profiles.
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Peralta, J. G. B., F. B. Elegado, J. F. Simbahan, I. G. Pajares, and E. I. Dizon. "Microbial and metabolite profiles of spontaneous and adjunct-inoculated cacao (Theobroma cacao L.) fermentation." Food Research 5, no. 2 (March 28, 2021): 331–39. http://dx.doi.org/10.26656/fr.2017.5(2).526.
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The succession of the dominant microbial population during cacao fermentation with or without adjunct inoculation of yeast and lactic acid bacteria (LAB) were monitored on a laboratory scale using culture-dependent and culture-independent methods. Yeasts and acetic acid bacteria (AAB) population throughout a five-day fermentation process showed no significant differences but the LAB population increased through adjunct inoculation. Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) identification method showed the dominance of only Lactobacillus plantarum, one of the species used as the adjunct inoculum, which resulted in higher lactic acid production. On the other hand, Acetobacter spp. and Gluconobacter spp. were markedly observed in the spontaneously fermented set-up resulting in increased acetic acid production, significantly different (p>0.05) at three to five days of fermentation. LAB and yeast inoculation resulted in a more desirable temperature and pH of the fermenting mash which may result in better product quality.
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De la Torre-González, Francisco Javier, José Alberto Narváez-Zapata, Patricia Taillandier, and Claudia Patricia Larralde-Corona. "Mezcal as a Novel Source of Mixed Yeasts Inocula for Wine Fermentation." Processes 8, no. 10 (October 16, 2020): 1296. http://dx.doi.org/10.3390/pr8101296.
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Mezcal yeasts were evaluated for their potential as grape-juice fermenters, characterizing their fermentation performance, both in terms of primary and volatile metabolites. Experiments were first carried-out in a semi-synthetic medium and then on grape juice, and population dynamics of the chosen mixed inoculum was assessed in grape juice. Accordingly, we initially tested 24 mezcal yeasts belonging to ten different species, and chose those that were more productive and stress tolerant for the mixed (dual) inoculum, having a final selection of three Saccharomyces cerevisiae strains (plus Fermichamp, a commercial wine strain) and three non-Saccharomyces strains, belonging to Kluyveromyces marxianus, Torulaspora delbrueckii, and Zygosaccharomyces bailii species. For the combination S. cerevisiae/T. delbrueckii (Sc/Td) mixed inoculum, we observed increasing isoamyl alcohol and phenyl ethyl acetate concentrations, as compared with the use of individual Saccharomyces strains, which resulted in a fruitier aroma profile. Alcohol final concentration was in average lower for the Sc/Td inoculum (fermentation power, FP, 13.6) as compared with the individual mezcal Saccharomyces strains (FP 14.3), and it was the highest when Td was co-cultured with the commercial strain (FP 14.6). Overall, our results show the feasibility of using yeasts isolated from mezcal as a novel source of inoculum for wine-type fermentation.
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Luo, Siyi (Rossie), Timothy A. DeMarsh, Dana deRiancho, Alina Stelick, and Samuel D. Alcaine. "Characterization of the Fermentation and Sensory Profiles of Novel Yeast-Fermented Acid Whey Beverages." Foods 10, no. 6 (May 27, 2021): 1204. http://dx.doi.org/10.3390/foods10061204.
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Acid whey is a by-product generated in large quantities during dairy processing, and is characterized by its low pH and high chemical oxygen demand. Due to a lack of reliable disposal pathways, acid whey currently presents a major sustainability challenge to the dairy industry. The study presented in this paper proposes a solution to this issue by transforming yogurt acid whey (YAW) into potentially palatable and marketable beverages through yeast fermentation. In this study, five prototypes were developed and fermented by Kluyveromyces marxianus, Brettanomyces bruxellensis, Brettanomyces claussenii, Saccharomyces cerevisiae (strain: Hornindal kveik), and IOC Be Fruits (IOCBF) S. cerevisiae, respectively. Their fermentation profiles were characterized by changes in density, pH, cell count, and concentrations of ethanol and organic acids. The prototypes were also evaluated on 26 sensory attributes, which were generated through a training session with 14 participants. While S. cerevisiae (IOCBF) underwent the fastest fermentation (8 days) and B. claussenii the slowest (21 days), K. marxianus and S. cerevisiae (Hornindal kveik) showed similar fermentation rates, finishing on day 20. The change in pH of the fermentate was similar for all five strains (from around 4.45 to between 4.25 and 4.31). Cell counts remained stable throughout the fermentation for all five strains (at around 6 log colony-forming units (CFU)/mL) except in the case of S. cerevisiae (Hornindal kveik), which ultimately decreased by 1.63 log CFU/mL. B. bruxellensis was the only strain unable to utilize all of the sugars in the substrate, with residual galactose remaining after fermentation. While both S. cerevisiae (IOCBF)- and B. claussenii-fermented samples were characterized by a fruity apple aroma, the former also had an aroma characteristic of lactic acid, dairy products, bakeries and yeast. A chemical odor characteristic of petroleum, gasoline or solvents, was perceived in samples fermented by B. bruxellensis and K. marxianus. An aroma of poorly aged or rancid cheese or milk also resulted from B. bruxellensis fermentation. In terms of appearance and mouthfeel, the S. cerevisiae (IOCBF)-fermented sample was rated the cloudiest, with the heaviest body. This study provides a toolkit for product development in a potential dairy-based category of fermented alcoholic beverages, which can increase revenue for the dairy industry by upcycling the common waste product YAW.
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Raymond Eder, María Laura, and Alberto Luis Rosa. "Non-Conventional Grape Varieties and Yeast Starters for First and Second Fermentation in Sparkling Wine Production Using the Traditional Method." Fermentation 7, no. 4 (December 20, 2021): 321. http://dx.doi.org/10.3390/fermentation7040321.
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Sparkling wine production using the traditional method involves a second fermentation of still wines in bottles, followed by prolonged aging on lees. The key factors affecting the organoleptic profiles of these wines are the grape varieties, the chemical and sensory attributes of the base wines elaborated, the yeast strains used for first and second fermentation, and the winery practices. While Chardonnay and Pinot noir are gold standard grape varieties in sparkling wine production, other valuable grape cultivars are used worldwide to elaborate highly reputable sparkling wines. Fundamental research on the chemical and sensory profiles of innovative sparkling wines produced by the traditional method, using non-conventional grape varieties and novel yeast strains for first and/or second fermentation, is accompanying their market diversification. In this review, we summarize relevant aspects of sparkling wine production using the traditional method and non-conventional grape varieties and yeast starters.
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Collar, C. "Review: Biochemical and technological assessment of the metabolism of pure and mixed cultures of yeast and lactic acid bacteria in breadmaking applications / Revisión: Aspectos bioquímicos y tecnológicos del metabolismo de cultivos puros y mixtos de levaduras y bacterias ácido lácticas en panificación." Food Science and Technology International 2, no. 6 (December 1996): 349–67. http://dx.doi.org/10.1177/108201329600200601.
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The production of varieties of breads with the quality required at present by the European consumer closely relates to the proper use of starting microorganisms in controlled and optimized breadmaking conditions. The relationship between processing requirements and wheat bread quality involves an understanding of the metabolism of the starting microflora which regulate production or assimilation of suitable and unsuitable metabolites during the breadmaking process, mediated by the specific enzyme activities and nutritional requirements of yeast and lactic acid bacteria. In this paper, recent advances in the biochemical and technological assessment of pure and mixed cultures of yeast and lactic acid bacteria in breadmaking applications are reviewed. Metabolite profiles in model and simplified wheat flour systems, performance of breadmaking starters in straight and sourdough systems, and relationships between process conditions, tech nological performance and metabolism of fermentation starters are discussed.
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Choi, Han-Sol, Keum-Yun Ha, Xing-Yue Xu, Hee-Cheol Kang, Hoon Kim, and Yeon-Ju Kim. "Off-Flavor Removal from Sheep Placenta via Fermentation with Novel Yeast Strain Brettanomyces deamine kh3 Isolated from Traditional Apple Vinegar." Molecules 26, no. 19 (September 26, 2021): 5835. http://dx.doi.org/10.3390/molecules26195835.
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Animal placentae can be used as health-promoting food ingredients with various therapeutic efficacies, but their use is limited by their unpleasant odor and taste. This study aimed to investigate the possibility of deodorization of sheep placenta via yeast fermentation. A yeast strain was successfully isolated and identified as a novel Brettanomyces strain (Brettanomyces deamine kh3). The deodorizing efficacy of fermentation of the sheep placenta with B. deamine kh3 was evaluated by 42 panels, based on evaluation of preference, ranking, and aroma profiles, and compared with normal placenta and placenta fermented with B. bruxellensis. The results of the sensory evaluation indicated that fermentation of the sheep placenta with B. deamine kh3 may improve its palatability by increasing flavors such as that of grass (tree), rubber, and burnt, and by decreasing the odor and soy sauce flavor. Solid-phase microextraction-gas chromatography (SPME-GC) showed that major off-flavors in sheep placenta, such as ammonia, dimethyl disulfide, and 1,3-dioxolane, were completely diminished in the sheep placenta fermented with B. deamine kh3. This study presents those major volatile compounds, including 2-isobutyl\-4,4-dimethyl-1,3-dioxane, and 3-methyl-1-butanol, could be crucial in improving the palatability of the sheep placentae fermented with B. deamine kh3. This study provides a good starting point for the industrial application of a new deodorization method.
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Michou, Savvoula, Erminta Tsouko, Eleni-Stavroula Vastaroucha, Panagiota Diamantopoulou, and Seraphim Papanikolaou. "Growth Potential of Selected Yeast Strains Cultivated on Xylose-Based Media Mimicking Lignocellulosic Wastewater Streams: High Production of Microbial Lipids by Rhodosporidium toruloides." Fermentation 8, no. 12 (December 7, 2022): 713. http://dx.doi.org/10.3390/fermentation8120713.
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The potential of Rhodosporidium toruloides, Candida oleophila, Metschnikowia pulcherima, and Cryptococcus curvatus species to produce single-cell-oil (SCO) and other valuable metabolites on low-cost media, based on commercial-type xylose, was investigated. Rhodosporidium strains were further evaluated in shake-flasks using different lignosulphonate (LS) concentrations, in media mimicking waste streams derived from the paper and pulp industry. Increasing the LS concentration up to 40 g/L resulted in enhanced dry cell weight (DCW) while SCO production increased up to ~5.0 g/L when R. toruloides NRRL Y-27012 and DSM 4444 were employed. The intra-cellular polysaccharide production ranged from 0.9 to 2.3 g/L in all fermentations. Subsequent fed-batch bioreactor experiments with R. toruloides NRRL Y-27012 using 20 g/L of LS and xylose, led to SCO production of 17.0 g/L with maximum lipids in DCW (YL/X) = 57.0% w/w. The fatty acid (FA) profile in cellular lipids showed that oleic (50.3–63.4% w/w) and palmitic acid (23.9–31.0%) were the major FAs. Only SCO from batch trials of R. toruloides strains contained α-linolenic acid. Media that was supplemented with various LS concentrations enhanced the unsaturation profile of SCO from R. toruloides NRRL Y-27012. SCO from R. toruloides strains could replace plant-based commodity oils in oleochemical-operations and/or it could be micro- and nano-encapsulated into novel food-based formulas offering healthier food-products.
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Gnoinski, Gail B., Simon A. Schmidt, Dugald C. Close, Karsten Goemann, Terry L. Pinfold, and Fiona L. Kerslake. "Novel Methods to Manipulate Autolysis in Sparkling Wine: Effects on Yeast." Molecules 26, no. 2 (January 13, 2021): 387. http://dx.doi.org/10.3390/molecules26020387.
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Sparkling wine made by the traditional method (Méthode Traditionelle) develops a distinct and desirable flavour and aroma profile attributed to proteolytic processes during prolonged ageing on lees. Microwave, ultrasound and addition of β-glucanase enzymes were applied to accelerate the disruption of Saccharomyces cerevisiae, and added to the tirage solution for secondary fermentation in traditional sparkling winemaking. Scanning electron microscopy and flow cytometry analyses were used to observe and describe yeast whole-cell anatomy, and cell integrity and structure via propidium iodide (PI) permeability after 6-, 12- and 18-months post-tirage. Treatments applied produced features on lees that were distinct from that of the untreated control yeast. Whilst control yeast displayed budding cells (growth features) with smooth, cavitated and flat external cell appearances; microwave treated yeast cells exhibited modifications like ‘doughnut’ shapes immediately after treatment (time 0). Similar ‘doughnut’-shaped and ‘pitted/porous’ cell features were observed on progressively older lees from the control. Flow cytometry was used to discriminate yeast populations; features consistent with cell disruption were observed in the microwave, ultrasound and enzyme treatments, as evidenced by up to 4-fold increase in PI signal in the microwave treatment. Forward and side scatter signals reflected changes in size and structure of yeast cells, in all treatments applied. When flow cytometry was interpreted alongside the scanning electron microscopy images, bimodal populations of yeast cells with low and high PI intensities were revealed and distinctive ‘doughnut’-shaped cell features observed in association with the microwave treatment only at tirage, that were not observed until 12 months wine ageing in older lees from the control. This work offers both a rapid approach to visualise alterations to yeast cell surfaces and a better understanding of the mechanisms of yeast lysis. Microwave, ultrasound or β-glucanase enzymes are tools that could potentially initiate the release of yeast cell compounds into wine. Further investigation into the impact of such treatments on the flavour and aroma profiles of the wines through sensory evaluation is warranted.
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Postigo, Vanesa, Margarita García, Juan Mariano Cabellos, and Teresa Arroyo. "Wine Saccharomyces Yeasts for Beer Fermentation." Fermentation 7, no. 4 (November 30, 2021): 290. http://dx.doi.org/10.3390/fermentation7040290.
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Multiple studies in recent years have shown the potential of Saccharomyces wild yeasts to produce craft beers with new flavour profiles and other desirable properties. Yeasts isolated from food (wine, bread, kombucha…) have shown potential promise for application in brewing. The aim of this study is to evaluate the ability of 141 Saccharomyces yeast strains isolated from the Madrilenian agriculture (from grapes, must, wine, vineyard, and cellars) to produce a novel ale beer. Fermentation activity of the strains was compared against the commercial strain Saccharomyces cerevisiae Safale S-04. In addition to the other aspects such as melatonin production, thirty-three volatile compounds belonging to higher alcohols, esters, aldehydes/cetones, acids, lactones and phenolic groups, were analysed by GC for selection of the strains. Ten strains were finally chosen, among which the most relevant was the strain G 520 showing a higher production of esters, higher alcohols and acids compared with S-04. The apparent attenuation for this strain was lower than commercial strain, which translates into more residual sugars. Furthermore, G 520 was more capable of producing significantly higher amounts of melatonin studied by HPLC, as well as showing a higher antioxidant capacity. Consumer study showed that G 520 strain could be used to produce a potential beer that has a place in the current market.
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Lindsay, Melodie A., Ninna Granucci, David R. Greenwood, and Silas G. Villas-Boas. "Fermentative Production of Volatile Metabolites Using Brettanomyces bruxellensis from Fruit and Vegetable By-Products." Fermentation 8, no. 9 (September 12, 2022): 457. http://dx.doi.org/10.3390/fermentation8090457.
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Natural sources of flavour and aroma compounds are highly sought by the modern consumer; however, traditional sources are often low-yielding, and global supply is often outstripped by consumer demand. Fermentation is a favourable route by which natural flavours and fragrances can be produced. A non-Saccharomyces yeast, Brettanomyces bruxellensis, was investigated for its fermentative potential for the production of flavour and aroma metabolites from juice industry by-products: apple pomace, carrot pomace, and orange pomace. Submerged solid-substrate fermentations were carried out using sterile by-products without nutrient supplementation. Gas chromatography–mass spectrometry was used for volatile metabolite profiling of fermented substrates. One compound of interest, phenylethyl alcohol (rose fragrance), was extracted and quantified using GC-MS at a yield of 2.68 g/kg wet carrot pomace weight. This represents a novel, natural production strategy for phenylethyl alcohol compared to the traditional steam distillation of Rosa domascus sp. petals.
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Vance, Arianne, Shilpa Raut, Adeline Grier-Welch, Nima Alamdari, and Mastaneh Sharafi. "Synergistic Effect of a Novel Combination of Pre-, Pro-, and Postbiotics on Microbial Fermentation and Metabolite Production In Vitro." Current Developments in Nutrition 6, Supplement_1 (June 2022): 1034. http://dx.doi.org/10.1093/cdn/nzac069.039.
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Abstract Objectives To test the effect of probiotic strains (Lactobacillus rhamnosus GG and Bifidobacterium animalis subsp. lactis BB-12; PS), a prebiotic (bacteriophage blend; BB), a postbiotic (tributyrin; TB), or a combination of all three (full mix; FM) on microbial fermentation and metabolite production in vitro. Methods Short term colonic incubation was performed under conditions representative of the proximal large intestine, using the fecal microbiota of a single healthy human donor. At the start of the experiment, treatments and a blank control (BC), were added to the reactors. Each reactor also received a carbohydrate-supplemented nutritional medium and freshly prepared fecal inoculum. Reactors were closed with a rubber septum, made anaerobic through flushing with nitrogen, and incubated for 48 hours. Each condition was run in triplicate. Overall fermentative activity (pH and gas production), changes in microbial metabolite production (short chain fatty acid, lactate, and ammonium analysis) were assessed. Results In the first 6 hours, microbial fermentation occurred in all treatments, indicated by pH shifts and production of gas and lactate. FM, PS, and BB stimulated production of lactate compared to BC (p < 0.05). After 24 hours, FM, PS and TB stimulated production of butyrate compared to BC (p < 0.05). FM and PS yielded more lactate than either BB or TB (p < 0.05). After 48 hours, FM, PS, BB, and TB each stimulated production of butyrate compared to BC (p < 0.05). Additionally, FM yielded significantly more butyrate than PS, TB, or BB (p < 0.05). Conclusions All treatments resulted in similar pH profiles and were representative of ideal conditions for bacterial growth and metabolism. The increased production of lactate in FM and PS was attributed to the fermentative activities of probiotics LGG and BB-12. Each treatment stimulated production of butyrate compared to BC but the largest increase in butyrate production was seen in FM, indicating a synergistic relationship between pre-, pro-, and postbiotics. Funding Sources The study was conducted by an independent lab, ProDigest, and funded and sponsored by Ritual (Natals, Inc.). Compound Solutions, Inc. also financially supported the study.
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Methner, Yvonne, Philipp Dancker, Robin Maier, Mailen Latorre, Mathias Hutzler, Martin Zarnkow, Martin Steinhaus, Diego Libkind, Stephanie Frank, and Fritz Jacob. "Influence of Varying Fermentation Parameters of the Yeast Strain Cyberlindnera saturnus on the Concentrations of Selected Flavor Components in Non-Alcoholic Beer Focusing on (E)-β-Damascenone." Foods 11, no. 7 (April 2, 2022): 1038. http://dx.doi.org/10.3390/foods11071038.
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The diversification of beer flavor is becoming increasingly popular, especially in the field of non-alcoholic beers, where sales are growing steadily. While flavor substances of traditional beers can largely be traced back to defined secondary metabolites, the production of non-alcoholic beers with non-Saccharomyces yeasts generates novel fruity flavors, some of which cannot yet be assigned to specific flavor substances. In a recently published study, besides pear, cool mint sweets, and banana-like flavor, distinctive red berry and apple flavors were perceived in a non-alcoholic beer fermented with the yeast strain Cyberlindnera saturnus TUM 247, whose secondary metabolites were to be elucidated in this study. The trials were carried out using response surface methodology to examine the fermentation properties of the yeast strain and to optimize the beer with maximum fruitiness but minimal off-flavors and ethanol content. It turned out that a low pitching rate, a moderate fermentation temperature, and an original gravity of 10.5 °P gave the optimal parameters. Qualitative analysis of the secondary metabolites, in addition to standard analysis for traditional beers, was first performed using headspace-gas chromatography with olfactometry. (E)-β-damascenone emerged as the decisive substance for the red berry and apple flavor and so this substance was then quantitated. Although (E)-β-damascenone is a well-known secondary metabolite in beer and this substance is associated with apple or cooked apple- and berry-like flavors, it has not yet been reported as a main flavor component in non-alcoholic beers.
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Catallo, Martina, Fabrizio Iattici, Cinzia L. Randazzo, Cinzia Caggia, Kristoffer Krogerus, Frederico Magalhães, Brian Gibson, and Lisa Solieri. "Hybridization of Saccharomyces cerevisiae Sourdough Strains with Cryotolerant Saccharomyces bayanus NBRC1948 as a Strategy to Increase Diversity of Strains Available for Lager Beer Fermentation." Microorganisms 9, no. 3 (March 2, 2021): 514. http://dx.doi.org/10.3390/microorganisms9030514.
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The search for novel brewing strains from non-brewing environments represents an emerging trend to increase genetic and phenotypic diversities in brewing yeast culture collections. Another valuable tool is hybridization, where beneficial traits of individual strains are combined in a single organism. This has been used successfully to create de novo hybrids from parental brewing strains by mimicking natural Saccharomycescerevisiae ale × Saccharomyceseubayanus lager yeast hybrids. Here, we integrated both these approaches to create synthetic hybrids for lager fermentation using parental strains from niches other than beer. Using a phenotype-centered strategy, S. cerevisiae sourdough strains and the S. eubayanus × Saccharomyces uvarum strain NBRC1948 (also referred to as Saccharomyces bayanus) were chosen for their brewing aptitudes. We demonstrated that, in contrast to S. cerevisiae × S. uvarum crosses, hybridization yield was positively affected by time of exposure to starvation, but not by staggered mating. In laboratory-scale fermentation trials at 20 °C, one triple S. cerevisiae × S. eubayanus × S. uvarum hybrid showed a heterotic phenotype compared with the parents. In 2 L wort fermentation trials at 12 °C, this hybrid inherited the ability to consume efficiently maltotriose from NBRC1948 and, like the sourdough S. cerevisiae parent, produced appreciable levels of the positive aroma compounds 3-methylbutyl acetate (banana/pear), ethyl acetate (general fruit aroma) and ethyl hexanoate (green apple, aniseed, and cherry aroma). Based on these evidences, the phenotype-centered approach appears promising for designing de novo lager beer hybrids and may help to diversify aroma profiles in lager beer.
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Takagi, Hiroshi, Miki Takaoka, Akari Kawaguchi, and Yoshito Kubo. "Effect of l-Proline on Sake Brewing and Ethanol Stress in Saccharomyces cerevisiae." Applied and Environmental Microbiology 71, no. 12 (December 2005): 8656–62. http://dx.doi.org/10.1128/aem.71.12.8656-8662.2005.
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ABSTRACT During the fermentation of sake, cells of Saccharomyces cerevisiae are exposed to high concentrations of ethanol, thereby damaging the cell membrane and functional proteins. l-Proline protects yeast cells from damage caused by freezing or oxidative stress. In this study, we evaluated the role of intracellular l-proline in cells of S. cerevisiae grown under ethanol stress. An l-proline-accumulating laboratory strain carries a mutant allele of PRO1, pro1 D154N, which encodes the Asp154Asn mutant γ-glutamyl kinase. This mutation increases the activity of γ-glutamyl kinase and γ-glutamyl phosphate reductase, which catalyze the first two steps of l-proline synthesis and which together may form a complex in vivo. When cultured in liquid medium in the presence of 9% and 18% ethanol under static conditions, the cell viability of the l-proline-accumulating laboratory strain is greater than the cell viability of the parent strain. This result suggests that intracellular accumulation of l-proline may confer tolerance to ethanol stress. We constructed a novel sake yeast strain by disrupting the PUT1 gene, which is required for l-proline utilization, and replacing the wild-type PRO1 allele with the pro1 D154N allele. The resultant strain accumulated l-proline and was more tolerant to ethanol stress than was the control strain. We used the strain that could accumulate l-proline to brew sake containing five times more l-proline than what is found in sake brewed with the control strain, without affecting the fermentation profiles.
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Fuess, Lucas Tadeu, Marcelo Zaiat, and Claudio Augusto Oller do Nascimento. "Novel insights on the versatility of biohydrogen production from sugarcane vinasse via thermophilic dark fermentation: Impacts of pH-driven operating strategies on acidogenesis metabolite profiles." Bioresource Technology 286 (August 2019): 121379. http://dx.doi.org/10.1016/j.biortech.2019.121379.
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Casimiro, Bruno, Inês Mota, Paula Veríssimo, Jorge Canhoto, and Sandra Correia. "Enhancing the Production of Hydrolytic Enzymes in Elicited Tamarillo (Solanum betaceum Cav.) Cell Suspension Cultures." Plants 12, no. 1 (January 2, 2023): 190. http://dx.doi.org/10.3390/plants12010190.
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Plant cell suspension cultures are widely used as a tool for analyzing cellular and molecular processes, metabolite synthesis, and differentiation, bypassing the structural complexity of plants. Within the range of approaches used to increase the production of metabolites by plant cells, one of the most recurrent is applying elicitors capable of stimulating metabolic pathways related to defense mechanisms. Previous proteomics analysis of tamarillo cell lines and cell suspension cultures have been used to further characterize and optimize the growth and stress-related metabolite production under in vitro controlled conditions. The main objective of this work was to develop a novel plant-based bioreactor system to produce hydrolytic enzymes using an elicitation approach. Based on effective protocols for tamarillo micropropagation and plant cell suspension culture establishment from induced callus lines, cell growth has been optimized, and enzymatic activity profiles under in vitro controlled conditions characterized. By testing different sucrose concentrations and the effects of two types of biotic elicitors, it was found that 3% (w/v) sucrose concentration in the liquid medium enhanced the production of hydrolytic enzymes. Moreover, casein hydrolysate at 0.5 and 1.5 g/L promoted protein production, whereas yeast extract (0.5 g/L) enhanced glycosidase activity. Meanwhile, chitosan (0.05 and 0.1 g/L) enhanced glycosidases, alkaline phosphates, and protease activities.
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Păcularu-Burada, Bogdan, Mihaela Turturică, João Miguel Rocha, and Gabriela-Elena Bahrim. "Statistical Approach to Potentially Enhance the Postbiotication of Gluten-Free Sourdough." Applied Sciences 11, no. 11 (June 7, 2021): 5306. http://dx.doi.org/10.3390/app11115306.
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Fermented products are permanently under the attention of scientists and consumers, both due to nutritional importance and health promoting effects. The fermented functional foods contribute to a more balanced diet and increase the immune responses (among many other health effects) with positive implications for quality of life. In this sense, improving the sourdough’s fermentation to boost the biotic (postbiotic and paraprobiotic) properties of the sourdough-based products has positive impacts on the nutritional and functional properties of the final baked products. These enhanced sourdoughs can be obtained in controlled fermentation conditions and used as sourdough bread improvers or novel bioingredients. In this context, our work aimed to optimize, using statistical tools, a gluten-free sourdough based on chickpea, quinoa, and buckwheat fermentation with selected lactic acid bacteria (LAB) to enhance its postbiotic properties. The most important biotechnological parameters were selected by Plackett–Burman Design (PBD) and then Response Surface Methodology (RSM) was applied to evaluate the interactions between the selected factors to maximize the gluten-free sourdough’s properties. As a result, the optimized fermented sourdough had antimicrobial activity with inhibition ratios between 71 and 100% against the Aspergillus niger, Aspergillus flavus, Penicillium spp. molds and against the Bacillus spp endospore-forming Gram-positive rods. The optimized variant showed a total titratable acidity (TTA) of 40.2 mL NaOH 0.1N. Finally, the high-performance liquid chromatography (HPLC) analysis highlighted a heterofermentative profile for the organic acids from the optimized sourdough. Among flavonoids and polyphenols, the level of caffeic and vanillic acids increased after lactic acid fermentation. The comparison between the optimized sourdough and the control evidenced significant differences in the metabolite profiles, thus highlighting its potential postbiotication effect.
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Philipp, Christian, Phillip Eder, Moritz Hartmann, Elsa Patzl-Fischerleitner, and Reinhard Eder. "Plant Fibers in Comparison with Other Fining Agents for the Reduction of Pesticide Residues and the Effect on the Volatile Profile of Austrian White and Red Wines." Applied Sciences 11, no. 12 (June 9, 2021): 5365. http://dx.doi.org/10.3390/app11125365.
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Pesticide residues in Austrian wines have so far been poorly documented. In 250 wines, 33 grape musts and 45 musts in fermentation, no limit values were exceeded, but in some cases high levels (>0.100 mg/L) of single residues were found, meaning that a reduction of these levels before bottling could make sense. In the course of this study, a white and a red wine were spiked with a mix of 23 pesticide residues from the group of fungicides (including botryticides), herbicides and insecticides. The influence of the following treatments on residue concentrations and volatile profiles were investigated: two activated charcoal products, a bentonite clay, two commercial mixed fining agents made of bentonite and charcoal, two yeast cell wall products, and a plant fiber-based novel filter additive. The results of this study show that all the agents tested reduced both residues and volatile compounds in wine, with activated charcoal having the strongest effect and bentonite the weakest. The mixed agents and yeast wall products showed less aroma losses than charcoal products, but also lower residue reduction. Plant fibers showed good reduction of pesticides with moderate aroma damage, but these results need to be confirmed under practical conditions.
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Iattici, Fabrizio, Martina Catallo, and Lisa Solieri. "Designing New Yeasts for Craft Brewing: When Natural Biodiversity Meets Biotechnology." Beverages 6, no. 1 (January 9, 2020): 3. http://dx.doi.org/10.3390/beverages6010003.
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Beer is a fermented beverage with a history as old as human civilization. Ales and lagers are by far the most common beers; however, diversification is becoming increasingly important in the brewing market and the brewers are continuously interested in improving and extending the range of products, especially in the craft brewery sector. Fermentation is one of the widest spaces for innovation in the brewing process. Besides Saccharomyces cerevisiae ale and Saccharomyces pastorianus lager strains conventionally used in macro-breweries, there is an increasing demand for novel yeast starter cultures tailored for producing beer styles with diversified aroma profiles. Recently, four genetic engineering-free approaches expanded the genetic background and the phenotypic biodiversity of brewing yeasts and allowed novel costumed-designed starter cultures to be developed: (1) the research for new performant S. cerevisiae yeasts from fermented foods alternative to beer; (2) the creation of synthetic hybrids between S. cerevisiae and Saccharomyces non-cerevisiae in order to mimic lager yeasts; (3) the exploitation of evolutionary engineering approaches; (4) the usage of non-Saccharomyces yeasts. Here, we summarized the pro and contra of these approaches and provided an overview on the most recent advances on how brewing yeast genome evolved and domestication took place. The resulting correlation maps between genotypes and relevant brewing phenotypes can assist and further improve the search for novel craft beer starter yeasts, enhancing the portfolio of diversified products offered to the final customer.
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del Fresno, Juan Manuel, Carlos Escott, Francisco Carrau, José Enrique Herbert-Pucheta, Cristian Vaquero, Carmen González, and Antonio Morata. "Improving Aroma Complexity with Hanseniaspora spp.: Terpenes, Acetate Esters, and Safranal." Fermentation 8, no. 11 (November 19, 2022): 654. http://dx.doi.org/10.3390/fermentation8110654.
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Hanseniaspora vineae and Hanseniaspora opuntiae are apiculate yeasts normally found on the skins of ripe grapes and at the beginning of alcoholic fermentation. Several studies have reported that these species can provide interesting sensory characteristics to wine by contributing high levels of acetate esters and can increase the mouthfeel and body of wines. The present work aims to evaluate the use of these two species sequentially with Saccharomyces cerevisiae to improve the sensory profile of Albillo Mayor white wines. The fermentations were carried out in triplicate in 150 L stainless steel barrels. At the end of the alcoholic fermentation polysaccharides, colour, and an extensive study of the aromatic profiles were measured. Results showed up to 1.55 times higher content of 2-phenylethanol in H. opuntiae wines and up to three times higher concentration of fermentative esters in H. vineae wines than in the controls. Interestingly, it should be noted that the compound safranal was identified only in the H. vineae wines. These results indicated that the species studied are an interesting bio-tool to improve the aromatic profile of Albillo Mayor white wines. A novel non-targeted NMR-based metabolomics approach is proposed as a tool for optimising wine productions with standard and sequential fermentation schemes using apiculate yeast strains due to its discriminant capacity to differentiate fine features between wine samples from the identical geographical origin and grape variety but diverse fermentations or vintages.
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Javed, Kiran, Qi Cheng, Adam Carroll, Thy Truong, and Stefan Bröer. "Development of Biomarkers for Inhibition of SLC6A19 (B0AT1)—A Potential Target to Treat Metabolic Disorders." International Journal of Molecular Sciences 19, no. 11 (November 14, 2018): 3597. http://dx.doi.org/10.3390/ijms19113597.
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Recent studies have established that dietary protein restriction improves metabolic health and glucose homeostasis. SLC6A19 (B0AT1) is the major neutral amino acid transporter in the intestine and carries out the bulk of amino acid absorption from the diet. Mice lacking SLC6A19 show signs of protein restriction, have improved glucose tolerance, and are protected from diet-induced obesity. Pharmacological blockage of this transporter could be used to induce protein restriction and to treat metabolic diseases such as type 2 diabetes. A few novel inhibitors of SLC6A19 have recently been identified using in vitro compound screening, but it remains unclear whether these compounds block the transporter in vivo. To evaluate the efficacy of SLC6A19 inhibitors biomarkers are required that can reliably detect successful inhibition of the transporter in mice. A gas chromatography mass spectrometry (GC-MS)-based untargeted metabolomics approach was used to discriminate global metabolite profiles in plasma, urine and faecal samples from SLC6A19ko and wt mice. Due to inefficient absorption in the intestine and lack of reabsorption in the kidney, significantly elevated amino acids levels were observed in urine and faecal samples. By contrast, a few neutral amino acids were reduced in the plasma of male SLC6A19ko mice as compared to other biological samples. Metabolites of bacterial protein fermentation such as p-cresol glucuronide and 3-indole-propionic acid were more abundant in SLC6A19ko mice, indicating protein malabsorption of dietary amino acids. Consistently, plasma appearance rates of [14C]-labelled neutral amino acids were delayed in SLC6A19ko mice as compared to wt after intra-gastric administration of a mixture of amino acids. Receiver operating characteristic (ROC) curve analysis was used to validate the potential use of these metabolites as biomarkers. These findings provide putative metabolite biomarkers that can be used to detect protein malabsorption and the inhibition of this transporter in intestine and kidney.
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de Bok, Frank A. M., Patrick W. M. Janssen, Jumamurat R. Bayjanov, Sander Sieuwerts, Arjen Lommen, Johan E. T. van Hylckama Vlieg, and Douwe Molenaar. "Volatile Compound Fingerprinting of Mixed-Culture Fermentations." Applied and Environmental Microbiology 77, no. 17 (July 8, 2011): 6233–39. http://dx.doi.org/10.1128/aem.00352-11.
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ABSTRACTWith the advent of the -omics era, classical technology platforms, such as hyphenated mass spectrometry, are currently undergoing a transformation toward high-throughput application. These novel platforms yield highly detailed metabolite profiles in large numbers of samples. Such profiles can be used as fingerprints for the accurate identification and classification of samples as well as for the study of effects of experimental conditions on the concentrations of specific metabolites. Challenges for the application of these methods lie in the acquisition of high-quality data, data normalization, and data mining. Here, a high-throughput fingerprinting approach based on analysis of headspace volatiles using ultrafast gas chromatography coupled to time of flight mass spectrometry (ultrafast GC/TOF-MS) was developed and evaluated for classification and screening purposes in food fermentation. GC-MS mass spectra of headspace samples of milk fermented by different mixed cultures of lactic acid bacteria (LAB) were collected and preprocessed in MetAlign, a dedicated software package for the preprocessing and comparison of liquid chromatography (LC)-MS and GC-MS data. The Random Forest algorithm was used to detect mass peaks that discriminated combinations of species or strains used in fermentations. Many of these mass peaks originated from key flavor compounds, indicating that the presence or absence of individual strains or combinations of strains significantly influenced the concentrations of these components. We demonstrate that the approach can be used for purposes like the selection of strains from collections based on flavor characteristics and the screening of (mixed) cultures for the presence or absence of strains. In addition, we show that strain-specific flavor characteristics can be traced back to genetic markers when comparative genome hybridization (CGH) data are available.
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Lawton II, James K., and Renu B. Kumar. "Characterization of water-types and their influence on the antimicrobial proper-ties of Kombucha ferments against bacteria and yeast." Fine Focus 2, no. 1 (January 1, 2016): 39–49. http://dx.doi.org/10.33043/ff.2.1.39-49.
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Understanding the relationships between diet, gut microflora, and health is an increasingly important area of research. Recent studies have demonstrated that Kombucha tea provides variable antimicrobial activity against pathogenic microbes. In this study, we tested Kombucha tea for antimicrobial activity against various Gram-positive and Gram-negative bacteria, as well as yeast, using an agar diffusion method. Standard zone of inhibition assays were used to test the hypothesis that variance in antimicrobial activity against Staphylococcus aureus, Escherichia coli and Candida albicans may be due to the varying levels of cations, like Ca2+, found in different water-types (well water, artesian water, city water, type-II water and distilled water). Inductively Coupled Plasma-Optical Emission Spectrometer (ICP-OES) results indicated that high cationic (Ca2+, Mg2+, and Na+) content water (well water) resulted in the largest zone of inhibition against S. aureus, with a 12.3% difference when compared to low cationic content water (type-II water). E. coli maintained a constant zone of inhibition regardless of water-type or batch-type, while C. albicans showed no zones of inhibition. Inhibition is either through a synergistic relationship with the pH conditions, the other cations present (Mg2+, Na+, Si, etc.) or a mix of both, as pH in the range of 4.5 - 3 is not enough to inhibit the growth of S. aureus. These results indicate that a direct relationship exists between cationic concentrations of water used to prepare Kombucha, and antibacterial activity against S. aureus, due to the improved fermentation of the tea with high concentrations of cations. Strong antimicrobial potential exists, particularly against S. aureus, which may be useful in determining novel approaches to synthesize antimicrobial drugs. Further study is needed to assess other S. aureus strains, as well as to determine how this relationship translates to human microbiota interactions and their microbial metabolic profiles.
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Ritalahti, Kirsti M., Shandra D. Justicia-Leon, Kathleen D. Cusick, Natalia Ramos-Hernandez, Michael Rubin, Jessica Dornbush, and Frank E. Löffler. "Sphaerochaeta globosa gen. nov., sp. nov. and Sphaerochaeta pleomorpha sp. nov., free-living, spherical spirochaetes." International Journal of Systematic and Evolutionary Microbiology 62, no. 1 (January 1, 2012): 210–16. http://dx.doi.org/10.1099/ijs.0.023986-0.
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Free-living bacteria with spherical cells 0.5–2.5 µm in diameter were isolated from freshwater sediment. 16S rRNA gene sequence analysis placed the new isolates within the phylum Spirochaetes (‘spirochaetes’). The isolates never displayed a helical morphology or motility. Growth occurred in the presence of 100 mg ampicillin l−1 in complex and defined mineral salts medium amended with vitamins, yeast extract and monosaccharides, disaccharides or soluble starch as fermentable substrates. Two distinct isolates, designated BuddyT and GrapesT, exhibited doubling times of 21±2 and 15±1 h in glucose-amended medium and grew at 15–37 and 15–30 °C. Optimum growth was observed between 25 and 30 °C and pH 6.5–7.5, with no growth below pH 5 or above pH 10. Hexose and pentose fermentation yielded ethanol, acetate and formate as major end products. Growth was strictly fermentative and anaerobic, but the isolates tolerated brief oxygen exposure. Nitrate, sulfate, thiosulfate and carbon dioxide were not used as electron acceptors, but soluble Fe(III) was reduced to Fe(II) in glucose-amended medium. The DNA G+C base contents of isolates BuddyT and GrapesT were 45.5–46.4 and 47.0–49.2 mol%, respectively. Phospholipid fatty acid (PLFA) profiles contained large proportions of C14 : 0 and C16 : 0 straight-chain saturated fatty acids; C16 : 1ω7c and C16 : 1ω9c dominated the mono-unsaturated PLFAs in isolate GrapesT, whereas isolate BuddyT also possessed C18 : 1ω5c, C18 : 1ω7c and C18 : 1ω9c fatty acids. Branched monoenoic acids accounted for up to 12.4 and 30 % of the total PLFA in isolates GrapesT and BuddyT, respectively. Based on their unique morphological features and the phylogenetic distance from their closest relatives, we propose the new genus, Sphaerochaeta gen. nov., to accommodate the new isolates within the novel species Sphaerochaeta globosa sp. nov. (type strain BuddyT = DSM 22777T = ATCC BAA-1886T) and Sphaerochaeta pleomorpha sp. nov. (type strain GrapesT = DSM 22778T = ATCC BAA-1885T). Sphaerochaeta globosa is the type species of the genus.
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Mattoo, Autar K., Sang Ho Chung, Ravinder K. Goyal, Tahira Fatima, Theophanes Solomos, Alka Srivastava, and Avtar K. Handa. "Overaccumulation of Higher Polyamines in Ripening Transgenic Tomato Fruit Revives Metabolic Memory, Upregulates Anabolism-Related Genes, and Positively Impacts Nutritional Quality." Journal of AOAC INTERNATIONAL 90, no. 5 (September 1, 2007): 1456–64. http://dx.doi.org/10.1093/jaoac/90.5.1456.
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Abstract Vegetables and fruits are essential components of the human diet as they are sources of vitamins, minerals, and fiber and provide antioxidants that prevent chronic diseases. Our goal is to improve durable nutritional quality of tomato fruit. We developed transgenic tomatoes expressing yeast S-adenosylmethionine decarboxylase (ySAMdc) gene driven by a fruit-specific E8 promoter to investigate the role of polyamines in fruit metabolism. Stable integration of E8-ySAMdc chimeric gene in tomato genome led to ripening-specific accumulation of polyamines, spermidine (Spd) and spermine (Spm), which in turn affected higher accumulation of glutamine, asparagine, and organic acids in the red fruit with significant decrease in the contents of valine, aspartate, sucrose, and glucose. The metabolite profiling analysis suggests that Spd/Spm are perceived as signaling organic-N metabolites by the fruit cells, resulting in the stimulation of carbon sequestration; enhanced synthesis of biomolecules; increased acid to sugar ratio, a good attribute for the fruit flavor; and in the accumulation of another vital amine, choline, which is an essential micronutrient for brain development. A limited transcriptome analysis of the transgenic fruit that accumulate higher polyamines revealed a large number of differentially expressed genes, about 55 of which represented discrete functional categories, and the remaining 45 were novel, unknown, or unclassified: amino acid biosynthesis, carotenoid biosynthesis, cell wall metabolism, chaperone family, flavonoid biosynthesis, fruit ripening, isoprenoid biosynthesis, polyamine biosynthesis, signal transduction, stress/defense-related, transcription, translation, and vacuolar function. There was a good correspondence between some gene transcripts and their protein products, but not in the case of the tonoplast intrinsic protein, which showed post-transcriptional regulation. Higher metabolic activity of the transgenic fruit is reflected in higher respiratory activity, and upregulation of chaperones and mitochondrial cytochrome oxidase transcripts compared to the control. These transgenic plants are a new resource to understand the role of Spd/Spm in fruit biology. Transcriptome analysis and metabolic profiles of Spd/Spm accumulating, transgenic fruit suggest the presence of an intricate regulation and interconnection between certain metabolic pathways that are revived when Spd and Spm likely reach a certain threshold. Thus, polyamines act as antiapoptotic regulatory molecules and are able to revive metabolic memory in the tomato fruit.
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Schlossarek, Dennis, Marcin Luzarowski, Ewelina M. Sokołowska, Venkatesh P. Thirumalaikumar, Lisa Dengler, Lothar Willmitzer, Jennifer C. Ewald, and Aleksandra Skirycz. "Rewiring of the protein–protein–metabolite interactome during the diauxic shift in yeast." Cellular and Molecular Life Sciences 79, no. 11 (October 15, 2022). http://dx.doi.org/10.1007/s00018-022-04569-8.
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AbstractIn budding yeast Saccharomyces cerevisiae, the switch from aerobic fermentation to respiratory growth is separated by a period of growth arrest, known as the diauxic shift, accompanied by a significant metabolic rewiring, including the derepression of gluconeogenesis and the establishment of mitochondrial respiration. Previous studies reported hundreds of proteins and tens of metabolites accumulating differentially across the diauxic shift transition. To assess the differences in the protein–protein (PPIs) and protein–metabolite interactions (PMIs) yeast samples harvested in the glucose-utilizing, fermentative phase, ethanol-utilizing and early stationary respiratory phases were analysed using isothermal shift assay (iTSA) and a co-fractionation mass spectrometry approach, PROMIS. Whereas iTSA monitors changes in protein stability and is informative towards protein interaction status, PROMIS uses co-elution to delineate putative PPIs and PMIs. The resulting dataset comprises 1627 proteins and 247 metabolites, hundreds of proteins and tens of metabolites characterized by differential thermal stability and/or fractionation profile, constituting a novel resource to be mined for the regulatory PPIs and PMIs. The examples discussed here include (i) dissociation of the core and regulatory particle of the proteasome in the early stationary phase, (ii) the differential binding of a co-factor pyridoxal phosphate to the enzymes of amino acid metabolism and (iii) the putative, phase-specific interactions between proline-containing dipeptides and enzymes of central carbon metabolism.
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Díaz-Muñoz, Cristian, Dario Van de Voorde, Andrea Comasio, Marko Verce, Carlos Eduardo Hernandez, Stefan Weckx, and Luc De Vuyst. "Curing of Cocoa Beans: Fine-Scale Monitoring of the Starter Cultures Applied and Metabolomics of the Fermentation and Drying Steps." Frontiers in Microbiology 11 (January 11, 2021). http://dx.doi.org/10.3389/fmicb.2020.616875.
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Starter culture-initiated cocoa fermentation processes can be applied to improve the quality of cured cocoa beans. However, an accurate monitoring of the microbial strains inoculated in fresh cocoa pulp-bean mass to assess their contribution to the cocoa bean curing process is still lacking. In the present study, eight different cocoa fermentation processes were carried out with Trinitario cocoa in vessels in Costa Rica to assess the contribution of two candidate yeast starter culture strains, namely Saccharomyces cerevisiae IMDO 050523 and Pichia kudriavzevii IMDO 020508, inoculated in combination with Limosilactobacillus fermentum IMDO 0611222 and Acetobacter pasteurianus IMDO 0506386. A multiphasic approach, consisting of culture-dependent selective plating and incubation, rRNA-PCR-DGGE community profiling of agar plate washes, and culture-independent high-throughput amplicon sequencing, combined with a metabolite target analysis of non-volatile and volatile organic compounds (VOCs), was performed on samples from the fermentation and/or drying steps. The different starter culture mixtures applied effectively steered the cocoa fermentation processes performed. Moreover, the use of an amplicon sequence variant (ASV) approach, aligning these ASVs to the whole-genome sequences of the inoculated strains, allowed the monitoring of these inoculated strains and their differentiation from very closely related variants naturally present in the background or spontaneous fermentation processes. Further, traits such as malolactic fermentation during the fermentation step and acetoin and tetramethylpyrazine formation during the drying step could be unraveled. Finally, the yeast strains inoculated influenced the substrate consumption and metabolite production during all starter culture-initiated fermentation processes. This had an impact on the VOC profiles of the cured cocoa beans. Whereas the P. kudriavzevii strain produced a wide range of VOCs in the cocoa pulp, the S. cerevisiae strain mostly influenced the VOC composition of the cured cocoa beans.
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Methner, Yvonne, Frederico Magalhães, Luis Raihofer, Martin Zarnkow, Fritz Jacob, and Mathias Hutzler. "Beer fermentation performance and sugar uptake of Saccharomycopsis fibuligera–A novel option for low-alcohol beer." Frontiers in Microbiology 13 (October 5, 2022). http://dx.doi.org/10.3389/fmicb.2022.1011155.
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There is a growing trend for beers with novel flavor profiles, as consumers demand a more diversified product range. Such beers can be produced by using non-Saccharomyces yeasts. The yeast species Saccharomycopsis fibuligera is known to produce exceptionally pleasant plum and berry flavors during brewer’s wort fermentation while its mycelia growth is most likely a technological challenge in industrial-scale brewing. To better understand and optimize the physiological properties of this yeast species during the brewing process, maltose and maltotriose uptake activity trials were performed. These revealed the existence of active transmembrane transporters for maltose in addition to the known extracellular amylase system. Furthermore, a single cell isolate of S. fibuligera was cultured, which showed significantly less mycelial growth during propagation and fermentation compared to the mother culture and would therefore be much more suitable for application on an industrial scale due to its better flocculation and clarification properties. Genetic differences between the two cultures could not be detected in a (GTG)5 rep-PCR fingerprint and there was hardly any difference in the fermentation process, sugar utilization and flavor profiles of the beers. Accordingly, the characteristic plum and berry flavor could also be perceived by using the culture from the single cell isolate, which was complemented by a dried fruit flavor. A fermentation temperature of 20°C at an original gravity of 10 °P proved to be optimal for producing a low-alcohol beer at around 0.8% (v/v) by applying the S. fibuligera yeast culture from the single cell isolate.
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Suntara, Chanon, Anusorn Cherdthong, Suthipong Uriyapongson, Metha Wanapat, and Pin Chanjula. "Novel Crabtree negative yeast from rumen fluids can improve rumen fermentation and milk quality." Scientific Reports 11, no. 1 (March 18, 2021). http://dx.doi.org/10.1038/s41598-021-85643-2.
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AbstractUpgrading the nutritive value of rice straw (RS) is necessary to increase its contribution to enhancing meat and milk production. Present work verified whether novel Crabtree negative yeast inoculant could promote RS utilization, rumen fermentation, and milk quality in tropical crossbred lactating Holstein cows. The new stain of Crabtree negative yeasts (Pichia kudriavzevii KKU20 and Candida tropicalis KKU20) was isolated from the rumen of dairy cattle. This study used 6 multiparous crossbreds between Holstein Frisian × Zebu dairy cows in their mid-lactation period. Dairy cows were randomly allocated to three ensiled RS with various yeast stains including Saccharomyces cerevisiae, P. kudriavzevii KKU20, and C. tropicalis KKU20 according to a 3 × 3 replicated Latin square design. Crabtree-negative yeast (P. kudriavzevii and C. tropicalis) increased the apparent digestibility of dry matter by about 6.9% when compared with Crabtree-positive yeast (S. cerevisiae). Bacterial populations were highest with ensiled RS by C. tropicalis KKU20. Ensiled RS with Crabtree-negative yeasts were significantly increased with total volatile fatty acids, but they did not affect volatile fatty acid profiles. Milk protein precentage was highest at 35.6 g/kg when C. tropicalis was fed, and lowest when applied with S. cerevisiae and P. kudriavzevii KKU20 in ensiled RS at 34.5 and 34.1 g/kg, respectively. Thus, feeding ensiled RS with novel Crabtree negative yeast could improve RS digestion, rumen fermentation, and milk protein content in dairy cows.
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So, Daniel, Chu K. Yao, Paul A. Gill, Naresh Pillai, Peter R. Gibson, and Jane G. Muir. "Screening dietary fibres for fermentation characteristics and metabolic profiles using a rapid in vitro approach: implications for irritable bowel syndrome." British Journal of Nutrition, October 8, 2020, 1–11. http://dx.doi.org/10.1017/s0007114520003943.
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Abstract The therapeutic value of specific fibres is partly dependent on their fermentation characteristics. Some fibres are rapidly degraded with the generation of gases that induce symptoms in patients with irritable bowel syndrome (IBS), while more slowly or non-fermentable fibres may be more suitable. More work is needed to profile a comprehensive range of fibres to determine suitability for IBS. Using a rapid in vitro fermentation model, gas production and metabolite profiles of a range of established and novel fibres were compared. Fibre substrates (n 15) were added to faecal slurries from three healthy donors for 4 h with gas production measured using real-time headspace sampling. Concentrations of SCFA and ammonia were analysed using GC and enzymatic assay, respectively. Gas production followed three patterns: rapid (≥60 ml/g over 4 h) for fructans, carrot fibre and maize-derived xylo-oligosaccharide (XOS); mild (30–60 ml/g) for partially hydrolysed guar gum, almond shell-derived XOS and one type of high-amylose resistant starch 2 (RS2) and minimal (no differences with blank controls) for methylcellulose, another high-amylose RS2, acetylated or butyrylated RS2, RS4, acacia gum and sugarcane bagasse. Gas production correlated positively with total SCFA (r 0·80, P < 0·001) and negatively with ammonia concentrations (r –0·68, P < 0·001). Proportions of specific SCFA varied: fermentation of carrot fibre, XOS and acetylated RS2 favoured acetate, while fructans favoured butyrate. Gas production and metabolite profiles differed between fibre types and within fibre classes over a physiologically relevant 4-h time course. Several fibres resisted rapid fermentation and may be candidates for clinical trials in IBS patients.
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Larralde-Corona, Claudia Patricia, Francisco Javier De la Torre-González, Pedro Alberto Vázquez-Landaverde, Dittmar Hahn, and José Alberto Narváez-Zapata. "Rational Selection of Mixed Yeasts Starters for Agave Must Fermentation." Frontiers in Sustainable Food Systems 5 (September 8, 2021). http://dx.doi.org/10.3389/fsufs.2021.684228.
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Tequila and mezcal are both traditional Mexican liquors that are produced from cooked Agave spp. must fermentation and usually rely on spontaneous or pure Saccharomyces cerevisiae strain inoculation. In order to contribute to the rational selection of yeast starters for tequila and mezcal productions, we tested a collection of 25 yeasts originally isolated from mezcal musts, spanning 10 different yeast species. These strains were first characterized in a semi synthetic medium (labeled as M2, having 90 g/L fructose and 10 g/L glucose of initial hexoses) at 48 h of culture, observing a differential pattern in the consumption of sugars and productivity. Selected Saccharomyces strains left around 10 g/L of fructose and showed higher fermentation performance. However, some non-Saccharomyces strains, specifically from Torulospora (Td), Kluyveromyces (Km), and Zygosaccharomyces (Zb) genera, consumed almost all the sugar (i.e., Km1Y9 with <5 g/L) and had a high productivity of ethanol. In general, all Saccharomyces strains presented a high production of ethyl-butyrate, ethyl-decanoate, and ethyl-hexanoate with peaks of 10, 38, and 3 μg/L, respectively. In addition, some Kluyveromyces and Torulospora strains showed a high production of phenyl ethyl acetate (i.e., Km1D5 with up to 1400 μg/L); isoamyl acetate (i.e., Km1D5 and Td1AN2 with more than 300 μg/L), and hexyl acetate (i.e., Td1AN2 with 0.3 μg/L). Representative strains of the most productive genera (Saccharomyces, Torulospora, and Kluyveromyces) were selected to evaluate their fermentative performance and survival in a mixed culture on a medium based on Agave tequilana must, and their population kinetics was characterized using specific fluorescent in situ hybridization (FISH) probes in a qualitative and semi-quantitative analysis during fermentation. We observed that the mixture ratios of 0.1:1:1 or 1:1:1 (Saccharomyces:Kluyveromyces:Torulospora), maintained good fermentation productivities, with alcohol yields above 0.45 g/g, and allowed a high survival rate of the non-Saccharomyces strains during the fermentation process. Finally, mixed inoculum fermentations on A. tequilana must medium, including different Saccharomyces strains and the finally selected Torulospora and Kluyveromyces strains, showed the best production parameters in terms of ethanol, carbon dioxide, glycerol, and acetic acid values, as well as improved volatile metabolite profiles as compared to the pure cultures. All these data were used to propose a methodology of selection of strains to be used as a pure or mixed starter for tequila and mezcal fermentations, with high primary metabolite productivity and desired aromatic profile.
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Bu, Ru, Bing Yan, Huijie Sun, Mengcheng Zhou, Huashan Bai, Xinghua Cai, Xueyan Mo, Guijiao Su, and Chengjian Jiang. "Copper Tolerance Mechanism of the Novel Marine Multi-Stress Tolerant Yeast Meyerozyma guilliermondii GXDK6 as Revealed by Integrated Omics Analysis." Frontiers in Microbiology 12 (November 18, 2021). http://dx.doi.org/10.3389/fmicb.2021.771878.
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Various agricultural products used in food fermentation are polluted by heavy metals, especially copper, which seriously endangers human health. Methods to remove copper with microbial strategies have gained interests. A novel Meyerozyma guilliermondii GXDK6 could survive independently under high stress of copper (1400 ppm). The copper tolerance mechanism of GXDK6 was revealed by integrated omics in this work. Whole-genome analysis showed that nine genes (i.e., CCC2, CTR3, FRE2, GGT, GST, CAT, SOD2, PXMP4, and HSP82) were related to GXDK6 copper tolerance. Copper stress elevated glutathione metabolism-related gene expression, glutathione content, and glutathione sulfur transferase activity, suggesting enhanced copper conjugation and detoxification in cells. The inhibited copper uptake by Ctr3 and enhanced copper efflux by Ccc2 contributed to the decrease in intracellular copper concentration. The improved expression of antioxidant enzyme genes (PXMP4, SOD2, and CAT), accompanied by the enhanced activities of antioxidant enzymes (peroxidase, superoxide dismutase, and catalase), decreased copper-induced reactive oxygen species production, protein carbonylation, lipid peroxidation, and cell death. The metabolite D-mannose against harsh stress conditions was beneficial to improving copper tolerance. This study contributed to understanding the copper tolerance mechanism of M. guilliermondii and its application in removing copper during fermentation.
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Vaštík, Peter, Zuzana Rosenbergová, Katarína Furdíková, Tatiana Klempová, Michal Šišmiš, and Daniela Šmogrovičová. "Potential of non-Saccharomyces yeast to produce non-alcoholic beer." FEMS Yeast Research, August 2, 2022. http://dx.doi.org/10.1093/femsyr/foac039.
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Abstract Recently, non-Saccharomyces yeast have become very popular in wine and beer fermentation. Their interesting abilities introduce novel aromatic profiles to the fermented product. In this study, screening of eight non-Saccharomyces yeast (Starmerella bombicola, Lindnera saturnus, Lindnera jadinii, ZygoSaccharomyces rouxii, Torulaspora delbrueckii, Pichia kluyveri, Candida pulcherrima, and Saccharomycodes ludwigii) revealed their potential in non-alcoholic beer production. Conditions for non-alcoholic beer production were optimised for all strains tested (except T. delbrueckii) with the best results obtained at temperature 10 to 15 °C for maximum of 10 days. Starmerella bombicola, an important industrial producer of biosurfactants, was used for beer production for the first time and was able to produce non-alcoholic beer even at 20 °C after 10 days of fermentation. Aromatic profile of the beer fermented with S. bombicola was neutral with no negative impact on organoleptic properties of the beer. The most interesting organoleptic properties were evaluated in beers fermented with L. jadinii and L. saturnus, which produced banana-flavoured beers with low alcohol content. This work confirmed the suitability of mentioned yeast to produce non-alcoholic beers and could serve as a steppingstone for further investigation.
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Chomvong, Kulika, Daniel I. Benjamin, Daniel K. Nomura, and Jamie H. D. Cate. "Cellobiose Consumption Uncouples Extracellular Glucose Sensing and Glucose Metabolism in Saccharomyces cerevisiae." mBio 8, no. 4 (August 8, 2017). http://dx.doi.org/10.1128/mbio.00855-17.
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ABSTRACT Glycolysis is central to energy metabolism in most organisms and is highly regulated to enable optimal growth. In the yeast Saccharomyces cerevisiae, feedback mechanisms that control flux through glycolysis span transcriptional control to metabolite levels in the cell. Using a cellobiose consumption pathway, we decoupled glucose sensing from carbon utilization, revealing new modular layers of control that induce ATP consumption to drive rapid carbon fermentation. Alterations of the beta subunit of phosphofructokinase-1 (PFK2), H+-plasma membrane ATPase (PMA1), and glucose sensors (SNF3 and RGT2) revealed the importance of coupling extracellular glucose sensing to manage ATP levels in the cell. Controlling the upper bound of cellular ATP levels may be a general mechanism used to regulate energy levels in cells, via a regulatory network that can be uncoupled from ATP concentrations under perceived starvation conditions. IMPORTANCE Living cells are fine-tuned through evolution to thrive in their native environments. Genome alterations to create organisms for specific biotechnological applications may result in unexpected and undesired phenotypes. We used a minimal synthetic biological system in the yeast Saccharomyces cerevisiae as a platform to reveal novel connections between carbon sensing, starvation conditions, and energy homeostasis. IMPORTANCE Living cells are fine-tuned through evolution to thrive in their native environments. Genome alterations to create organisms for specific biotechnological applications may result in unexpected and undesired phenotypes. We used a minimal synthetic biological system in the yeast Saccharomyces cerevisiae as a platform to reveal novel connections between carbon sensing, starvation conditions, and energy homeostasis.
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Martiniuk, Jonathan T., Jonah Hamilton, Thomas Dodsworth, and Vivien Measday. "Grape-associated fungal community patterns persist from berry to wine on a fine geographical scale." FEMS Yeast Research, January 2, 2023. http://dx.doi.org/10.1093/femsyr/foac067.
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Abstract Wine grape fungal community composition is influenced by abiotic factors including geography and vintage. Compositional differences may correlate with different wine metabolite composition and sensory profiles, suggesting a microbial role in the shaping of a wine's terroir, or regional character. While grape and wine-associated fungal community composition has been studied extensively at a regional and sub-regional scale, it has not been explored in detail on fine geographical scales over multiple harvests. Over two years, we examined the fungal communities on Vitis Vinifera cv. Pinot noir grape berry surfaces, in crushed grapes, and in lab spontaneous fermentations from three vineyards within a <1km radius in Canada's Okanagan Valley wine region. We also evaluated the effect of winery environment exposure on fungal community composition by sampling grapes crushed and fermented in the winery at commercial scale. Spatiotemporal community structure was evident among grape berry surface, crushed grape and fermentation samples, with each vineyard exhibiting a distinct fungal community signature. Crushed grape fungal populations were richer in fermentative yeast species compared to grape berry surface fungal populations. Our study suggests that, as on a regional level, fungal populations may contribute to fine-scale -terroir,” with significant implications for single-vineyard wines.
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Cheng, Yanfei, Hui Zhu, Zhengda Du, Xuena Guo, Chenyao Zhou, Zhaoyue Wang, and Xiuping He. "Eukaryotic translation factor eIF5A contributes to acetic acid tolerance in Saccharomyces cerevisiae via transcriptional factor Ume6p." Biotechnology for Biofuels 14, no. 1 (February 8, 2021). http://dx.doi.org/10.1186/s13068-021-01885-2.
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Abstract Background Saccharomyces cerevisiae is well-known as an ideal model system for basic research and important industrial microorganism for biotechnological applications. Acetic acid is an important growth inhibitor that has deleterious effects on both the growth and fermentation performance of yeast cells. Comprehensive understanding of the mechanisms underlying S. cerevisiae adaptive response to acetic acid is always a focus and indispensable for development of robust industrial strains. eIF5A is a specific translation factor that is especially required for the formation of peptide bond between certain residues including proline regarded as poor substrates for slow peptide bond formation. Decrease of eIF5A activity resulted in temperature-sensitive phenotype of yeast, while up-regulation of eIF5A protected transgenic Arabidopsis against high temperature, oxidative or osmotic stress. However, the exact roles and functional mechanisms of eIF5A in stress response are as yet largely unknown. Results In this research, we compared cell growth between the eIF5A overexpressing and the control S. cerevisiae strains under various stressed conditions. Improvement of acetic acid tolerance by enhanced eIF5A activity was observed all in spot assay, growth profiles and survival assay. eIF5A prompts the synthesis of Ume6p, a pleiotropic transcriptional factor containing polyproline motifs, mainly in a translational related way. As a consequence, BEM4, BUD21 and IME4, the direct targets of Ume6p, were up-regulated in eIF5A overexpressing strain, especially under acetic acid stress. Overexpression of UME6 results in similar profiles of cell growth and target genes transcription to eIF5A overexpression, confirming the role of Ume6p and its association between eIF5A and acetic acid tolerance. Conclusion Translation factor eIF5A protects yeast cells against acetic acid challenge by the eIF5A-Ume6p-Bud21p/Ime4p/Bem4p axles, which provides new insights into the molecular mechanisms underlying the adaptive response and tolerance to acetic acid in S. cerevisiae and novel targets for construction of robust industrial strains.
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Santra, Hiran K., and Debdulal Banerjee. "Broad-Spectrum Antimicrobial Action of Cell-Free Culture Extracts and Volatile Organic Compounds Produced by Endophytic Fungi Curvularia Eragrostidis." Frontiers in Microbiology 13 (June 23, 2022). http://dx.doi.org/10.3389/fmicb.2022.920561.
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Endophytes are the mutualistic microorganisms that reside within the host plant and promote plant growth in adverse conditions. Plants and their endophytes are engaged in a symbiotic relationship that enables endophytes to access bioactive genes of the ethnomedicinal plants, and, as a result, endophytes are constantly addressed in the sector of pharmaceuticals and agriculture for their multidomain bio-utility. The gradual increase of antimicrobial resistance can be effectively countered by the endophytic metabolites. In these circumstances, in the present investigation, endophytic Curvularia eragrostidis HelS1 was isolated from an ethnomedicinally valuable plant Helecteris isora from East India’s forests. The secondary volatile and non-volatile metabolites are extracted from HelS1 and are found to be effective broad-spectrum antimicrobials. A total of 26 secondary metabolites (9 volatiles and 17 non-volatiles) are extracted from the isolate, which exhibits effective antibacterial [against six Gram-positive and seven Gram-negative pathogens with a minimum inhibitory concentrations (MIC) value ranging from 12.5 to 400 μg ml–1] and antifungal (against seven fungal plant pathogens) activity. The secondary metabolite production was optimised by one variable at a time technique coupled with the response surface methodology. The results revealed that there was a 34% increase in antibacterial activity in parameters with 6.87 g L–1 of fructose (as a carbon source), 3.79 g L–1 of peptone (as a nitrogen source), pH 6.75, and an inoculation period of 191.5 h for fermentation. The volatile metabolite production was also found to be optimum when the medium was supplemented with yeast extract and urea (0.2 g L–1) along with dextrose (40 g L–1). Amongst extracted volatile metabolites, 1-H-indene 1 methanol acetate, tetroquinone, N, N-diphenyl-2-nitro-thio benzamide, Trans 1, 2-diethyl-trans-2-decalinol, naphthalene, and azulene are found to be the most effective. Our investigation opens up opportunities in the sector of sustainable agriculture as well as the discovery of novel antimicrobials against dreadful phyto and human pathogens.
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Giorello, Facundo, Maria Jose Valera, Valentina Martin, Andres Parada, Valentina Salzman, Laura Camesasca, Laura Fariña, et al. "Genomic and Transcriptomic Basis ofHanseniaspora vineae's Impact on Flavor Diversity and Wine Quality." Applied and Environmental Microbiology 85, no. 1 (October 26, 2018). http://dx.doi.org/10.1128/aem.01959-18.
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ABSTRACTHanseniasporais the main genus of the apiculate yeast group that represents approximately 70% of the grape-associated microflora.Hanseniaspora vineaeis emerging as a promising species for quality wine production compared to other non-Saccharomycesspecies. Wines produced byH. vineaewithSaccharomyces cerevisiaeconsistently exhibit more intense fruity flavors and complexity than wines produced byS. cerevisiaealone. In this work, genome sequencing, assembling, and phylogenetic analysis of two strains ofH. vineaeshowed that it is a member of theSaccharomycescomplex and it diverged before the whole-genome duplication (WGD) event from this clade. Specific flavor gene duplications and absences were identified in theH. vineaegenome compared to 14 fully sequenced industrialS. cerevisiaegenomes. The increased formation of 2-phenylethyl acetate and phenylpropanoids such as 2-phenylethyl and benzyl alcohols might be explained by gene duplications ofH. vineaearomatic amino acid aminotransferases (ARO8andARO9) and phenylpyruvate decarboxylases (ARO10). Transcriptome and aroma profiles under fermentation conditions confirmed these genes were highly expressed at the beginning of stationary phase coupled to the production of their related compounds. The extremely high level of acetate esters produced byH. vineaecompared to that byS. cerevisiaeis consistent with the identification of six novel proteins with alcohol acetyltransferase (AATase) domains. The absence of the branched-chain amino acid transaminases (BAT2) and acyl coenzyme A (acyl-CoA)/ethanolO-acyltransferases (EEB1) genes correlates withH. vineae’s reduced production of branched-chain higher alcohols, fatty acids, and ethyl esters, respectively. Our study provides sustenance for understanding and potentially utilizing genes that determine fermentation aromas.IMPORTANCEThe huge diversity of non-Saccharomycesyeasts in grapes is dominated by the apiculate genusHanseniaspora. Two native strains ofHanseniaspora vineaeapplied to winemaking because of their high oenological potential in aroma and fermentation performance were selected to obtain high-quality genomes. Here, we present a phylogenetic analysis and the complete transcriptome and aroma metabolome ofH. vineaeduring three fermentation steps. This species produced significantly richer flavor compound diversity thanSaccharomyces, including benzenoids, phenylpropanoids, and acetate-derived compounds. The identification of six proteins, different fromS. cerevisiaeATF, with diverse acetyltransferase domains inH. vineaeoffers a relevant source of native genetic variants for this enzymatic activity. The discovery of benzenoid synthesis capacity inH. vineaeprovides a new eukaryotic model to dilucidate an alternative pathway to that catalyzed by plants’ phenylalanine lyases.
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Geijer, Cecilia, Fábio Faria-Oliveira, Antonio D. Moreno, Simon Stenberg, Scott Mazurkewich, and Lisbeth Olsson. "Genomic and transcriptomic analysis of Candida intermedia reveals the genetic determinants for its xylose-converting capacity." Biotechnology for Biofuels 13, no. 1 (March 12, 2020). http://dx.doi.org/10.1186/s13068-020-1663-9.
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Abstract Background An economically viable production of biofuels and biochemicals from lignocellulose requires microorganisms that can readily convert both the cellulosic and hemicellulosic fractions into product. The yeast Candida intermedia displays a high capacity for uptake and conversion of several lignocellulosic sugars including the abundant pentose d-xylose, an underutilized carbon source since most industrially relevant microorganisms cannot naturally ferment it. Thus, C. intermedia constitutes an important source of knowledge and genetic information that could be transferred to industrial microorganisms such as Saccharomyces cerevisiae to improve their capacity to ferment lignocellulose-derived xylose. Results To understand the genetic determinants that underlie the metabolic properties of C. intermedia, we sequenced the genomes of both the in-house-isolated strain CBS 141442 and the reference strain PYCC 4715. De novo genome assembly and subsequent analysis revealed C. intermedia to be a haploid species belonging to the CTG clade of ascomycetous yeasts. The two strains have highly similar genome sizes and number of protein-encoding genes, but they differ on the chromosomal level due to numerous translocations of large and small genomic segments. The transcriptional profiles for CBS 141442 grown in medium with either high or low concentrations of glucose and xylose were determined through RNA-sequencing analysis, revealing distinct clusters of co-regulated genes in response to different specific growth rates, carbon sources and osmotic stress. Analysis of the genomic and transcriptomic data also identified multiple xylose reductases, one of which displayed dual NADH/NADPH co-factor specificity that likely plays an important role for co-factor recycling during xylose fermentation. Conclusions In the present study, we performed the first genomic and transcriptomic analysis of C. intermedia and identified several novel genes for conversion of xylose. Together the results provide insights into the mechanisms underlying saccharide utilization in C. intermedia and reveal potential target genes to aid in xylose fermentation in S. cerevisiae.
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Morinaga, Kana, Hiroyuki Kusada, Sachiko Sakamoto, Takumi Murakami, Atsushi Toyoda, Hiroshi Mori, Xian-Ying Meng, Motoko Takashino, Kazutoshi Murotomi, and Hideyuki Tamaki. "Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae." International Journal of Systematic and Evolutionary Microbiology 72, no. 10 (October 26, 2022). http://dx.doi.org/10.1099/ijsem.0.005596.
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Two strictly anaerobic, Gram-stain-positive, non-motile bacteria (strains OPF53T and TOC12T) were isolated from mouse intestines. Strains OPF53T and TOC12T grew at pH 5.5–9.0 and 5.0–9.0, respectively, and at temperatures of 30–45 °C. The cell morphologies of these strains were short rods and rods, respectively, and the cells possessed intracellular granules. The major cellular fatty acids of OPF53T were C18 : 1 cis 9 and C18 : 1 cis 9 dimethyl acetal, whereas those of TOC12T were C18 : 0 and C18 : 1 cis 9. In OPF53T, the main end-products of modified peptone–yeast extract–glucose (PYG) fermentation were lactate, formate and butyrate, whereas, in addition to these acids, TOC12T also produced hydrogen. The genomes of OPF53T and TOC12T were respectively 2.2 and 2.0 Mbp in size with a DNA G+C contents of 69.1 and 58.7 %. The 16S rRNA gene sequences of OPF53T and TOC12T showed the highest similarity to members of the family Atopobiaceae , namely, Olsenella phocaeensis Marseille-P2936T (94.3 %) and Olsenella umbonata KCTC 15140T (93.2 %), respectively. Phylogenetic analyses revealed that both isolates formed distinct lineages from other genera of the family Atopobiaceae . In addition, the two strains were characterized by relatively low 16S rRNA gene sequence similarity (93.4 %) and can be distinguished by their distinctive traits (including cell shape, DNA G+C content, and major fatty acids profiles). On the basis of their polyphasic taxonomic properties, these isolates represent two noel species of two novel genera within the family Atopobiaceae , for which the names Granulimonas faecalis gen. nov., sp. nov. (OPF53T=JCM 35015T=KCTC 25474T) and Leptogranulimonas caecicola gen. nov., sp. nov. (TOC12T=JCM 35017T=KCTC 25472T) are proposed.
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Uerlings, Julie, Ester Arévalo Sureda, Martine Schroyen, Kikianne Kroeske, Sofie Tanghe, Maartje De Vos, Geert Bruggeman, et al. "Impact of Citrus Pulp or Inulin on Intestinal Microbiota and Metabolites, Barrier, and Immune Function of Weaned Piglets." Frontiers in Nutrition 8 (December 3, 2021). http://dx.doi.org/10.3389/fnut.2021.650211.
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We investigated the use of citrus pulp (CP) as a novel prebiotic capable of exerting microbiota and immunomodulating capacities to alleviate weaning stress. Inulin (IN), a well-known prebiotic, was used for comparison. Hundred and 28 male weaned piglets of 21 days old were assigned to 32 pens of 4 piglets each. Piglets were assigned to one of the four treatments, i.e., control, IN supplemented at 0.2% (IN0.2%), and CP supplemented either at 0.2% (CP0.2%) or at 2% (CP2%). On d10–11 and d31–32 post-weaning, one pig per pen was euthanized for intestinal sampling to evaluate the growth performance, chyme characteristics, small intestinal morphology, colonic inflammatory response and barrier integrity, metabolite profiles [gas chromatography-mass spectrometry (GC-MS), and liquid chromatography-mass spectrometry (LC-MS)], and microbial populations. The IN treatment and the two CP treatments induced higher small intestinal villus height to crypt depth ratios in comparison with the control diet at both sampling times. All treatments decreased acidic goblet cell absolute counts in the crypts in comparison to the control diet of the duodenum on d10–11 and d31–32. The gene expression of β-defensin 2 was downregulated in colonic tissues following the IN and CP2% inclusion on d31–32. On d31–32, piglets fed with IN and CP0.2% showed lower mRNA levels of occludin and claudin-3, respectively. Not surprisingly, flavonoids were observed in the colon in the CP treatments. Increased colonic acetate proportions on d10–11, at the expense of branched-chain fatty acid (BCFA) levels, were observed following the CP2% supplementation compared to the control diet, inferring a reduction of proteolytic fermentation in the hindgut. The beneficial microbial community Faecalibacterium spp. was promoted in the colon of piglets fed with CP2% on d10–11 (p = 0.04; false discovery rate (FDR) non-significant) and on d31–32 (p = 0.03; FDR non-significant) in comparison with the control diet. Additionally, on d31–32, CP2% increased the relative abundance of Megasphaera spp. compared to control values (p = 0.03; FDR non-significant). In conclusion, CP2% promoted the growth of beneficial bacterial communities in both post-weaning time points, modulating colonic fermentation patterns in the colon. The effects of CP supplementation were similar to those of IN and showed the potential as a beneficial feed supplement to alleviate weaning stress.
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Quinn, Robert A., Jose A. Navas-Molina, Embriette R. Hyde, Se Jin Song, Yoshiki Vázquez-Baeza, Greg Humphrey, James Gaffney, et al. "From Sample to Multi-Omics Conclusions in under 48 Hours." mSystems 1, no. 2 (April 26, 2016). http://dx.doi.org/10.1128/msystems.00038-16.
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ABSTRACT Polymicrobial infections are difficult to diagnose due to the challenge in comprehensively cultivating the microbes present. Omics methods, such as 16S rRNA sequencing, metagenomics, and metabolomics, can provide a more complete picture of a microbial community and its metabolite production, without the biases and selectivity of microbial culture. However, these advanced methods have not been applied to clinical or industrial microbiology or other areas where complex microbial dysbioses require immediate intervention. The reason for this is the length of time required to generate and analyze omics data. Here, we describe the development and application of a pipeline for multi-omics data analysis in time frames matching those of the culture-based approaches often used for these applications. This study applied multi-omics methods effectively in clinically relevant time frames and sets a precedent toward their implementation in clinical medicine and industrial microbiology. Multi-omics methods have greatly advanced our understanding of the biological organism and its microbial associates. However, they are not routinely used in clinical or industrial applications, due to the length of time required to generate and analyze omics data. Here, we applied a novel integrated omics pipeline for the analysis of human and environmental samples in under 48 h. Human subjects that ferment their own foods provided swab samples from skin, feces, oral cavity, fermented foods, and household surfaces to assess the impact of home food fermentation on their microbial and chemical ecology. These samples were analyzed with 16S rRNA gene sequencing, inferred gene function profiles, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics through the Qiita, PICRUSt, and GNPS pipelines, respectively. The human sample microbiomes clustered with the corresponding sample types in the American Gut Project (http://www.americangut.org ), and the fermented food samples produced a separate cluster. The microbial communities of the household surfaces were primarily sourced from the fermented foods, and their consumption was associated with increased gut microbial diversity. Untargeted metabolomics revealed that human skin and fermented food samples had separate chemical ecologies and that stool was more similar to fermented foods than to other sample types. Metabolites from the fermented foods, including plant products such as procyanidin and pheophytin, were present in the skin and stool samples of the individuals consuming the foods. Some food metabolites were modified during digestion, and others were detected in stool intact. This study represents a first-of-its-kind analysis of multi-omics data that achieved time intervals matching those of classic microbiological culturing. IMPORTANCE Polymicrobial infections are difficult to diagnose due to the challenge in comprehensively cultivating the microbes present. Omics methods, such as 16S rRNA sequencing, metagenomics, and metabolomics, can provide a more complete picture of a microbial community and its metabolite production, without the biases and selectivity of microbial culture. However, these advanced methods have not been applied to clinical or industrial microbiology or other areas where complex microbial dysbioses require immediate intervention. The reason for this is the length of time required to generate and analyze omics data. Here, we describe the development and application of a pipeline for multi-omics data analysis in time frames matching those of the culture-based approaches often used for these applications. This study applied multi-omics methods effectively in clinically relevant time frames and sets a precedent toward their implementation in clinical medicine and industrial microbiology.