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431 results for “Fermentation”
Design of a new model yeast consortium for ecological studies of enological fermentation
<p>Dataset describing the characterization of a new 6-species yeast consortium representative of wine yeast diversity, as well as its application as proof-of-concept to explore the diversity-functionnality relationship in microbial community.</p> <p>It includes the data, scripts, figures, tables, and additional informations pertaining to the article "Design of a new model yeast consortium for ecological studies of enological fermentation" to be submitted.</p>
Supplementary Materials for Genomic insight into Pediococcus acidilactici HN9, a potential probiotic strain isolated from the traditional Thai-style fermented beef Nhang
<p>Figure S1: Subsystem information of the HN9 based on the RAST annotation server, <br> Figure S2: Phylogenetic analysis of Pediococcus acidilactici HN9 and other strains at the species level, Figure S3: Sequence alignment of Enterolysin A from Pediococcus pentosaceus ATCC 25745 with Enterolysin A identified in the HN9, <br> Figure S4: Identification of bacteriocin-encoding genes from all bacterial strains in the genus Pediococcus, <br> Table S1: The information of strain used in this study, <br> Table S2: Metadata of all strains used in this study.</p>
Snapgene files of the genetic constructions for Morella thermoacetica used in Task 2.2 (Advanced GMO preparation for gas (CO2/CO/H2) fermentation process)
<p>Part of WP2 these snapgene files of the genetic constructions for Morella thermoacetica were used in Task 2.2 (Advanced GMO preparation for gas (CO2/CO/H2) fermentation process). The strains we were able to construct were:</p> <p>1.- M. thermoacetica DSM 521 pK18ACSACassette complete<br>2.- M. thermoacetica DSM 521 pK18ACSACassette AatA<br>3.- M. thermoacetica DSM 2955 pK18ACSACassette PudL-AckA<br>4.- M. thermoacetica DSM 2955 pK18ACSACassette AatA</p> <p>To construct these strains CSIC used a modular synthetic construction carrying the regions up and down of the acsA gene to delete it. Within these regions, a gene cluster composed by the GmR, pduL, ackA and aatA genes, all of them controlled by the strong constitutional promoter of the glyceraldehyde 3-phosphate dehydrogenase gene from Moorella were inserted. The modular design of our recombinant cassette allows us to construct different cassettes with different gene combinations. In all cases, the acsA gene will be deleted and the acetate cannot be transformed back into acetyl-CoA:</p> <p>Cassette 1.- ACSA-GmR-pduL-ackA-aatA-ACSA: this is a complete cassette which carries the genes encoding the phosphotransacetylase, the acetate kinase and the acetate exporter. This strain should accumulate a higher concentration of acetate inside the cell that should be exported to the medium.</p> <p>Cassette 2.- ACSA-GmR-pduL-ackA-ACSA: this cassette lacks the transporter, so this strain should accumulate a higher concentration inside the cell. Then, the only way to prevent acetate toxicity is by increasing its own mechanisms to export this compound or by growing slower in order to manage acetate accumulation.</p> <p>Cassette 3.- ACSA-GmR-aatA-ACSA: this cassette only carries the acetate exporter, so virtually all the acetate produced inside the cell should be exported. This is another strategy to increase the metabolic flux inside the cell towards acetate without overexpressing any other gene of the acetate pathway, and at the same time avoiding toxicity problems.</p> <p>Cassette 4.- ACSA-GmR-ACSA: this cassette would generate an insertion mutant in which acsA is only replaced by the GmR encoding gene. This mutant should also generate a higher amount of acetate since it cannot be transformed back to acetyl-CoA.</p>
Data from: High temperatures and low soil moisture synergistically reduce switchgrass yields from marginal field sites and inhibit fermentation
<p>'Marginal lands' are low productivity sites abandoned from agriculture for reasons such as low or high soil water content, challenging topography, or nutrient deficiency. To avoid competition with crop production, cellulosic bioenergy crops have been proposed for cultivation on marginal lands, however on these sites they may be more strongly affected by environmental stresses such as low soil water content. In this study we used rainout shelters to induce low soil moisture on marginal lands and determine the effect of soil water stress on switchgrass growth and the subsequent production of bioethanol. Five marginal land sites that span a latitudinal gradient in Michigan and Wisconsin were planted to switchgrass in 2013 and during the 2018-2021 growing seasons were exposed to reduced precipitation under rainout shelters in comparison to ambient precipitation. The effect of reduced precipitation was related to the environmental conditions at each site and biofuel production metrics (switchgrass biomass yields and composition and ethanol production). During the first year (2018), the rainout shelters were designed with 60% rain exclusion, which did not affect biomass yields compared to ambient conditions at any of the field sites, but decreased switchgrass fermentability at the Wisconsin Central - Hancock site. In subsequent years, the shelters were redesigned to fully exclude rainfall, which led to reduced biomass yields and inhibited fermentation for three sites. When switchgrass was grown in soils with large reductions in moisture and increases in temperature, the potential for biofuel production was significantly reduced, exposing some of the challenges associated with producing biofuels from lignocellulosic biomass grown under drought conditions.</p>
Insights into intraspecific diversity of central carbon metabolites in Saccharomyces cerevisiae during wine fermentation
<p>Supplementary data including the data set used for the " Insights into intraspecific diversity of central carbon metabolites in <em>Saccharomyces cerevisiae</em> during wine fermentation" publication.</p> <p>Abstract:</p> <p><em>Saccharomyces cerevisiae</em>, as the workhorse of alcoholic fermentation, is a major actor in winemaking. In this context, this yeast species performs alcoholic fermentation to convert sugars from the grape must into ethanol and CO2 with outstanding efficiency as it reaches on average 92% of the maximum theoretical yield of conversion. Primary metabolites produced during fermentation have a great importance in wine where they significantly impact wine characteristics. While ethanol content contributes to the overall profile, others metabolites also have significant impacts, even when present in lower concentrations: glycerol, succinate, acetate, ⍺-ketoglutarate, lactate… <em>S. cerevisiae</em> is known for its great genetic diversity and plasticity that is directly related to its living environment, natural or technological and therefore to domestication. This leads to a wide phenotypic diversity of metabolites production. However, the range of metabolic diversity is variable and depends on the pathway considered. With the aim to improve wine quality, the selection, development and use of strains with dedicated metabolites production without genetic modifications can rely on the already existing natural diversity. Here we detail a screening experiment that aims to assess the diversity of primary metabolites production in a set of 51 <em>S. cerevisiae</em> strains from various genetic backgrounds (wine, flor, rum, West African, sake…). To approximate winemaking conditions, we used a synthetic grape must as fermentation medium and measured seven metabolites by HPLC. Results pointed out great yield differences between strains depending on the metabolite considered. Ethanol appeared as the one with the smallest variation among our set of strains, although it was by far the most produced. A clear negative correlation between ethanol and glycerol was observed, confirming glycerol synthesis as a suitable lever to reduce ethanol yield. Genetic groups were linked to specific metabolic yields such as high α-ketoglutarate and low acetate yields for wine strains. This study thus helps to characterise the phenotypic diversity of <em>S. cerevisiae</em> in a wine-like context and comforts the use of natural diversity in the development of new strains. Finally, it provides a detailed data set usable to study diversity of well known (ethanol, glycerol, acetate) or little-known (lactate) primary metabolites production, including in common commercial wine strains.</p> <p> </p> <p> </p>
Effects of yeast strain and juice nitrogen status on glutathione utilisation during fermentation of model media
<p><strong>Background and Aims</strong></p> <p>An OIV resolution provides guidelines on using glutathione as a prefermentation additive when the amount of yeast assimilable nitrogen (YAN) of a juice or must is adequate, to avoid the metabolism of glutathione by the yeast. The effect of YAN concentration on glutathione metabolism by yeast had not been determined. This study explored whether nitrogen management could be used to control glutathione consumption during fermentation.</p> <p><strong>Methods and Results</strong></p> <p>An HPLC-UV method was developed to quantify reduced L-glutathione (GSH) and oxidised glutathione (GSSG) and used to monitor yeast GSH metabolism during alcoholic fermentation with two yeast strains (AWRI 1688 and AWRI 2861). The addition of GSH had no impact on the fermentation rate of the chemically defined medium, even in a limited YAN environment; however, a decrease in glutathione concentration occurred regardless of YAN concentration. The effect of GSH on volatile sulfur compound formation was yeast strain-dependent.</p> <p><strong>Conclusions</strong></p> <p>Increasing the YAN status of a chemically defined medium led to a decrease in GSH consumption during fermentation, but the loss of GSH could not be prevented entirely, even with a low initial GSH concentration and high initial YAN.</p> <p><strong>Significance of the Study</strong></p> <p>In the presence of higher concentrations of GSH during fermentation, there is a risk of forming undesirable fermentative sulfur compounds that are not mitigated through nitrogen supplementation. Thus, it seems unlikely that an argument could be made for the inclusion of GSH in relevant food standards codes as a wine additive especially if a lack of GSH metabolism was a criterion.</p>
Figure 1 in Chironomids also favour fermented products: an observation of chironomids dwelling in rotten apples
Figure 1. Pictures of the study pond (a), rotten apples floating on the surface (b), some of the apples before sectioning (c), and a larva of Endochironomus cf. tendens found inside the apple (d). Photo L. Hamerlik.
Isotopic nitrogen fractionation and fermentation products from invitro culture experiments using rumen bacteria
<p>Dataset used in the paper titled : The extent of nitrogen isotopic fractionation in rumen bacteria is associated with changes in rumen nitrogen metabolism (DOI: 10.21203/rs.3.rs-2350552/v1). It contains individual data for isotopic nitrogen fractionation and fermentation products from invitro culture experiments using rumen bacteria</p>
Effects of yeast strain and juice nitrogen status on glutathione utilisation during fermentation of model media
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Data from: High temperatures and low soil moisture synergistically reduce switchgrass yields from marginal field sites and inhibit fermentation
Open the record for dataset details and reuse information.
Dataset for Black Tea Fermentation Detection based on Image Processing and Machine Learning Techniques
<p>This is a dataset on black tea fermentation. The dataset contains black tea fermentation conditions and images. The fermentation conditions captured are: temperature, humidty and time. The images belong to black tea as they underwent the fermentation process. The dataset was collected in Sisibo tea factory, Kenya in July and August 2020.</p>
Distributed flux balance analysis simulations of serial biomass fermentation by two organisms
<p><span>Intelligent biorefinery design that addresses both the composition of the biomass feedstock as well as fermentation microorganisms could benefit from dedicated tools for computational simulation and computer-assisted optimization. Here we present the BioLego Vn2.0 framework, based on Microsoft Azure Cloud, which supports large-scale simulations of biomass serial fermentation processes by two different organisms. BioLego enables the simultaneous analysis of multiple fermentation scenarios and the comparison of fermentation potential of multiple feedstock compositions. Thanks to the effective use of cloud computing it further allows resource intensive analysis and exploration of media and organism modifications. We use BioLego to obtain biological and validation results, including (1) exploratory search for the optimal utilization of corn biomasses – corn cobs, corn fiber and corn stover – in fermentation biorefineries; (2) analysis of the possible effects of changes in the composition of <i>K. alvarezi</i> biomass on the ethanol production yield in an anaerobic two-step process (<i>S. cerevisiae</i> followed by <i>E. coli</i>); (3) analysis of the impact, on the estimated ethanol production yield, of knocking out single organism reactions either in one or in both organisms in an anaerobic two-step fermentation process of <i>Ulva</i> sp. into ethanol (<i>S. cerevisiae</i> followed by <i>E. coli</i>); and (4) comparison of several experimentally measured ethanol fermentation rates with the predictions of BioLego.</span></p>
Data from: Microbial composition play the leading role in volatile fatty acid production in the fermentation of different scale of corn stover with rumen fluid
<p>Rumen fluid is a natural and green biocatalyst that can efficiently degrade biomass into volatile fatty acid (VFA) used to produce value-added materials. But the essence of high degradation efficiency in the rumen has not been fully analyzed. This study investigated the contribution of substrate structure and microbial composition to volatile fatty acid production in the fermentation of corn stover. The ball milled corn stover were innovatively applied to ferment with the rumen fluid collected at different digestion times. Exogeneous cellulase was also added to the ruminal fermentation to further reveal the inner mechanism. With prolonged digestion time, the microbial community relative abundance levels of Bacteroidetes and Firmicutes increased from 29.98% to 72.74% and decreased from 51.76% to 22.11%, respectively. The highest VFA production of the corn stover was achieved via treatment with the rumen fluid collected at 24 h which was up to 9508 mg/L. The ball milled corn stover achieved high VFA production because of the more accessible substrate structure. The application of exogenous cellulase has no significant influence to the ruminal fermentation. The microbial community abundance contributed more to the VFA production compared with the substrate structures.</p>
Supplementary dataset and tables for "Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale"
<p><strong>Supplementary dataset and tables for "Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale"</strong></p> <p><strong>Supplementary Dataset and Tables</strong> listing identified acetone biosynthesis genes from mining of the DJ collection and gene and part sequences used for combinatorial library and cell-free prototyping (<strong>Supplementary Tab. 1</strong>), combinatorial library combinations and results (<strong>Supplementary Tab. 2</strong>), gene KO predictions (<strong>Supplementary Tab. 3</strong>), cell-free prototyping combinations and results (<strong>Supplementary Tab. 4</strong>), proteomics results for wild-type strain plus acetone biosynthesis plasmid (<strong>Supplementary Tab. 5</strong>), proteomics results for strain Δ<em>0553</em> plus select combinatorial library plasmids (<strong>Supplementary Tab. 6</strong>), Genbank accession numbers for 272 genomes (<strong>Supplementary Tab. 7</strong>). sequences of oligonucleotides (<strong>Supplementary Tab. 8</strong>) and emission factors used to calculate the GHG emissions of acetone (<strong>Supplementary Tab. 9</strong>) and IPA (<strong>Supplementary Tab. 10</strong>) in LCA.</p>
Supplementary files to "Potential of Fermentation and Vacuum Packaging Followed by Chilling to Preserve Black Soldier Fly Larvae (Hermetia illucens)"
Open the record for dataset details and reuse information.
Bioprospecting for bioactive peptide production by lactic acid bacteria isolated from fermented dairy food
<p>Table S1 of the review article "Bioprospecting for bioactive peptide production by lactic acid bacteria isolated from fermented dairy food"</p> <p>by Davide Tagliazucchi, Serena Martini and Lisa Solieri</p>
Fig. 1 in Heleomyzidae and Lauxaniidae (Diptera, Brachycera, Acalyptrata) trapped in the Czech Republic with syrup and fermented fruit
Fig. 1: A schematic map of localities. Locality from Slovakia is not included.
Dataset supporting the paper "Effect of prebiotic fermentation products from primary human gut microbiota on an in vitro intestinal model"
<p>Short chain fatty acids (SCFA) originate from the bacterial fermentation of dietary fibre in the gastrointestinal tract. They are hypothesised to play a key role in microbiota–gut–brain crosstalk and the effect of individual SCFAs or mixtures thereof has been broadly studied. However, studies using fermentation products to evaluate the effect of microbiota-targeted interventions, such as prebiotics, probiotics, or diet, are sparse, particularly in humans. In addition, the complexity of these physiological processes translates as a challenge for their simulation<em> in vitro</em>. In this work, fermentation products of prebiotic-enriched media by bacteria present in primary human faecal samples were tested using an epithelium model based on a Caco-2/HT29-MTX co-culture. The prebiotics raftilose and fructo-oligosaccharides (FOS) were tested and the experimental conditions (contact time and minimal dilution) optimised to avoid cytotoxicity. None of the conditions tested compromised the intestinal epithelium integrity as verified by the TEER and the expression of the tight junction-specific protein – occludin. In addition, none of the fermentation products caused an inflammatory response as determinedby the expression of inflammatory genes by qRT-PCR. The products of fermentation of media enriched with FOS showed a moderate protective effect against the formation of reactive oxygen species. This work provides an important basis for the development of <em>in vitro</em> models using a simple approach to evaluate host-gut microbiota interactions, using co-cultures of intestinal cell lines and products of <em>in vitro</em> fermentations by primary human gut microbiota. </p>
Phenotypic variations of primary metabolites yield during alcoholic fermentation in the Saccharomyces cerevisiae species
<p>Supplementary data including the data set used for the" Phenotypic variations of primary metabolites yield during alcoholic fermentation in the Saccharomyces cerevisiae species" publication.</p> <p> </p> <p>Abstract:</p> <p><em>Saccharomyces cerevisiae</em>, as the workhorse of alcoholic fermentation, is a major actor of winemaking. In this context, this yeast species performs alcoholic fermentation to convert sugars from the grape must into ethanol and CO<sub>2</sub> with an outstanding efficiency: it reaches on average 92% of the maximum theoretical yield of conversion. Primary metabolites produced during fermentation stand for a great importance in wine where they significantly impact wine characteristics. Ethanol indeed does, but others too, which are found in lower concentrations: glycerol, succinate, acetate, ⍺-ketoglutarate… Their production, which can be characterised by a yield according to the amount of sugars consumed, is known to differ from one strain to another. <em>S. cerevisiae</em> is known for its great genetic diversity and plasticity that is directly related to its living environment, natural or technological and therefore to domestication. This leads to a great phenotypic diversity of metabolites production. However, the range of metabolic diversity is variable and depends on the pathway considered. In the aim to improve wine quality, the selection, development and use of strains with dedicated metabolites production without genetic modifications can rely on the natural diversity that already exists. Here we detail a screening that aims to assess this diversity of primary metabolites production in a set of 51 <em>S. cerevisiae</em> strains from various genetic backgrounds (wine, flor, rum, West African, sake…). To approach winemaking conditions, we used a synthetic grape must as fermentation medium and measured by HPLC five main metabolites. Results obtained pointed out great yield differences between strains and that variability is dependent on the metabolite considered. Ethanol appears as the one with the smallest variation among our set of strains, despite it’s by far the most produced. A clear negative correlation between ethanol and glycerol yields has been observed, confirming glycerol synthesis as a good lever to impact ethanol yield. Genetic groups have been identified as linked to high production of specific metabolites, like succinate for rum strains or alpha-ketoglutarate for wine strains. This study thus helps to define the phenotypic diversity of <em>S. cerevisiae</em> in a wine-like context and supports the use of ways of development of new strains exploiting natural diversity. Finally, it provides a detailed data set usable to study diversity of primary metabolites production, including common commercial wine strains.</p>
Transient acetaldehyde production by SO2 producing S. cerevisiae promotes survival of Oenococcus oeni during co-fermentation
<p>Stuck or sluggish malolactic fermentation (MLF) can be problematic in limiting wine conditions, particularly white and sparkling base musts / wines. In these cases, knowledge of yeast-bacteria strain compatibility and the amount of sulfur dioxide (SO<sub>2</sub>) a yeast strain produces are important considerations for successful MLF.</p> <p>Here, the effects of yeast-derived SO<sub>2</sub> production on <em>O. oeni</em> survival was investigated in laboratory- and pilot-scale co-fermentations in Chardonnay. Further to the <em>S</em>. <em>cerevisiae</em> strain affecting <em>O. oeni</em> survival and MLF, we show that SO<sub>2</sub> production by yeast (to approximately 65 mg/L) can be uncoupled from <em>O. oeni </em>survival in early stages of co-fermentation. Bacterial survival with certain SO<sub>2</sub>-producing yeast strains was correlated with early, transient formation of a high concentration of acetaldehyde. Upon co-inoculation, an extremely low concentration range (approximately 1–44 µg/L) of calculated molecular SO<sub>2</sub> is indicated to regulate <em>O</em>. <em>oeni</em> survival. <span>Possible strain-dependent sensitivity of <em>O. oeni</em> to bound SO<sub>2</sub> may also occur, although the extent and nature of such inhibition by the SO<sub>2</sub> adduct itself during co-fermentation remains unclear. </span></p> <p><span>Choice of co-inoculation yeast strain also influenced wine diacetyl concentration, </span>which was only detected in wines co-inoculated with high-SO<sub>2</sub>-producing <em>S. cerevisiae </em>strains. <span>These wines also had comparatively high citation frequency for a buttery sensory attribute. </span>Both the SO<sub>2</sub> and acetaldehyde production capacity of yeasts are therefore seen as meaningful co-inoculation selection criteria. <span>The range of yeast strains suitable for MLF induction by co-inoculation could be widened to include SO<sub>2</sub>-producing strains which transiently produce an early, high concentration of acetaldehyde. Reliance on total / bound SO<sub>2</sub> concentration may also potentially provide an inaccurate measure of SO<sub>2</sub> toxicity towards <em>O. oeni</em>, particularly for co-inoculation, and the impact of low, equilibrium concentrations of molecular SO<sub>2</sub> should also be considered. </span></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.