Project description:Palm wine is obtained by fermentation of palm tree sap. In the Pacific coast of Mexico, palm wine is called Tuba and it is consumed as a traditional fermented beverage. Tuba has empirical applications such as an auxiliary in gastrointestinal diseases and a good source of nutrients. In the present study, a next-generation sequencing of the V3-V4 regions of the 16S rRNA gene was employed to analyze bacterial diversity and population dynamics during the fermentation process of Tuba, both in laboratory controlled conditions and in commercial samples from local vendors. Taxonomic identification showed that Fructobacillus was the main genus in all the samples, following by Leuconostoc, Gluconacetobacter, Sphingomonas, and Vibrio. Alpha diversity analysis demonstrated variability between all the samples. Beta diversity clustered the bacterial population according to the collection origin of the sample. Metabolic functional profile inference showed that the members of the bacterial communities may present the vitamin, antibiotic and antioxidant biosynthesis genes. Additionally, we further investigated the correlation between the predominant genera and some composition parameters of this beverage. This study provides the basis of the bacterial community composition and functionality of the fermented beverage.
Project description:Black waxy rice wine fermentation metabolites are closely related to the product's final quality. However, little is known about dynamic metabolite changes during fermentation. Here, we used gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) metabolomics and multivariate statistical analysis to explore the relationship between metabolites and fermentation time. A total of 159 metabolites were identified during the entire fermentation process. The PCA analysis revealed a clear separation between the samples after 4 days and 2 days, and the samples after 4-24 days clustered together. This indicated that BGRW fermentation progresses rapidly in the first 48 hr of fermentation. A total of 40 metabolites were identified as differential during fermentation (VIP > 1 and p < .05), including 12 organic acids, four amino acids, one fatty acid, 17 sugars and sugar alcohols, one alcohol, and five other metabolites. Pathway analysis showed that the differential metabolites were involved in 28 metabolic pathways, and the most commonly influenced pathways (impact value > 0.1 and p < .05) were galactose metabolism, pyruvate metabolism; starch and sucrose metabolism; alanine, aspartic acid, and glutamate metabolism; the tricarboxylic acid cycle, glyoxylic acid, and dicarboxylic acid metabolism; and amino sugar and nucleotide sugar metabolism. Moreover, the integrated metabolic pathway was generated to understand the transformation and accumulation of differential metabolites. Overall, these results provide a comprehensive overview of metabolite changes during black waxy rice wine fermentation.
Project description:Comparative gene expression analysis of two wine yeast strains at three time points (days 2, 5 and 14) during fermentation of colombar must. In our study we conducted parallel fermentations with the VIN13 and BM45 wine yeast strains in two different media, namely MS300 (syntheticmust) and Colombar must. The intersection of transcriptome datasets from both MS300 (simulated wine must;GSE11651) and Colombar fermentations should help to delineate relevant and ‘noisy’ changes in gene expression in response to experimental factors such as fermentation stage and strain identity.
Project description:Physicochemical changes in fermented alcoholic beverages are significantly related to microbial community development during fermentation. Due to its unusually long fermentation, Gayangju, a traditional Korean house rice wine fermented with nuruk as the traditional starter, gives rise to a strong yeast community and, therefore, a high ethanol concentration and different flavors. However, no detailed analysis has been examined. Changes in microbial community structure during Gayangju fermentation were examined using both culture-dependent and culture-independent methods. During fermentation, Saccharomyces cerevisiae and Saccharomycopsis fibuligera were dominant during all stages of the fermentation. In contrast, Candida parapsilosis, Hanseniaspora guilliermondii, Pichia anomala, Malassezia cuniculi and P. fermentans were identified as minor. P. anomala appeared after the second brewing and then remained constant. Among the 19 compounds identified in this study as order-active compounds, 2-methyl-1-butanol (isoamyl alcohol) was the major compound that increased during the long fermentation stage. Most of the odor-active compounds such as 2,3-butanediol, 3-methyl-1-butanol, ethyl tetradecanoate, ethyl decanoate, ethyl dodecanoate, butanoic acid, 3-methylbutanoic acid (isovaleric acid), 2-methylbutanoic acid, 2-methyl-1-propanol, ethyl acetate, ethyl caprylate, 2-phenylethanol, and 3-methylbutyl acetate increased as the fermentation progressed during 68 days of fermentation, which showed significant differences in the concentrations of odor-active compounds of commercially fermented makgeolli.
Project description:In this study, genome-wide expression analyses were used to study the response of Saccharomyces cerevisiae to stress throughout a 15-day wine fermentation. Forty per cent of the yeast genome significantly changed expression levels to mediate long-term adaptation to fermenting grape must. Among the genes that changed expression levels, a group of 223 genes was identified, which was designated as fermentation stress response (FSR) genes that were dramatically induced at various points during fermentation. FSR genes sustain high levels of induction up to the final time point and exhibited changes in expression levels ranging from four- to 80-fold. The FSR is novel; 62% of the genes involved have not been implicated in global stress responses and 28% of the FSR genes have no functional annotation. Genes involved in respiratory metabolism and gluconeogenesis were expressed during fermentation despite the presence of high concentrations of glucose. Ethanol, rather than nutrient depletion, seems to be responsible for entry of yeast cells into the stationary phase.
Project description:Date palm (Phoenix dactylifera L.) is a cultivated woody plant species with agricultural and economic importance. Here we report a genome assembly for an elite variety (Khalas), which is 605.4?Mb in size and covers >90% of the genome (~671?Mb) and >96% of its genes (~41,660 genes). Genomic sequence analysis demonstrates that P. dactylifera experienced a clear genome-wide duplication after either ancient whole genome duplications or massive segmental duplications. Genetic diversity analysis indicates that its stress resistance and sugar metabolism-related genes tend to be enriched in the chromosomal regions where the density of single-nucleotide polymorphisms is relatively low. Using transcriptomic data, we also illustrate the date palm's unique sugar metabolism that underlies fruit development and ripening. Our large-scale genomic and transcriptomic data pave the way for further genomic studies not only on P. dactylifera but also other Arecaceae plants.
Project description:During fermentative growth in natural and industrial environments, Saccharomyces cerevisiae must redistribute the available nitrogen from multiple exogenous sources to amino acids in order to suitably fulfill anabolic requirements. To exhaustively explore the management of this complex resource, we developed an advanced strategy based on the reconciliation of data from a set of stable isotope tracer experiments with labeled nitrogen sources. Thus, quantifying the partitioning of the N compounds through the metabolism network during fermentation, we demonstrated that, contrary to the generally accepted view, only a limited fraction of most of the consumed amino acids is directly incorporated into proteins. Moreover, substantial catabolism of these molecules allows for efficient redistribution of nitrogen, supporting the operative de novo synthesis of proteinogenic amino acids. In contrast, catabolism of consumed amino acids plays a minor role in the formation of volatile compounds. Another important feature is that the α-keto acid precursors required for the de novo syntheses originate mainly from the catabolism of sugars, with a limited contribution from the anabolism of consumed amino acids. This work provides a comprehensive view of the intracellular fate of consumed nitrogen sources and the metabolic origin of proteinogenic amino acids, highlighting a strategy of distribution of metabolic fluxes implemented by yeast as a means of adapting to environments with changing and scarce nitrogen resources.IMPORTANCE A current challenge for the wine industry, in view of the extensive competition in the worldwide market, is to meet consumer expectations regarding the sensory profile of the product while ensuring an efficient fermentation process. Understanding the intracellular fate of the nitrogen sources available in grape juice is essential to the achievement of these objectives, since nitrogen utilization affects both the fermentative activity of yeasts and the formation of flavor compounds. However, little is known about how the metabolism operates when nitrogen is provided as a composite mixture, as in grape must. Here we quantitatively describe the distribution through the yeast metabolic network of the N moieties and C backbones of these nitrogen sources. Knowledge about the management of a complex resource, which is devoted to improvement of the use of the scarce N nutrient for growth, will be useful for better control of the fermentation process and the sensory quality of wines.
Project description:The identification of natural allelic variations controlling quantitative traits could contribute to decipher metabolic adaptation mechanisms within different populations of the same species. Such variations could result from human-mediated selection pressures and participate to the domestication. In this study, the genetic causes of the phenotypic variability of the central carbon metabolism of Saccharomyces cerevisiae were investigated in the context of the enological fermentation. The genetic determinism of this trait was found out by a quantitative trait loci (QTL) mapping approach using the offspring of two strains belonging to the wine genetic group of the species. A total of 14 QTL were identified from which 8 were validated down to the gene level by genetic engineering. The allelic frequencies of the validated genes within 403 enological strains showed that most of the validated QTL had allelic variations involving flor yeast specific alleles. Those alleles were brought in the offspring by one parental strain that contains introgressions from the flor yeast genetic group. The causative genes identified are functionally linked to quantitative proteomic variations that would explain divergent metabolic features of wine and flor yeasts involving the tricarboxylic acid cycle (TCA), the glyoxylate shunt and the homeostasis of proton and redox cofactors. Overall, this work led to the identification of genetic factors that are hallmarks of adaptive divergence between flor yeast and wine yeast in the wine biotope. These results also reveal that introgressions originated from intraspecific hybridization events promoted phenotypic variability of carbon metabolism observed in wine strains.