Wine production is a complex process from the vineyard to the winery. On this journey, microbes play a decisive role. From the environment where the vines grow, encompassing soil, topography, weather ...and climate through to management practices in vineyards, the microbes present can potentially change the composition of wine. Introduction of grapes into the winery and the start of winemaking processes modify microbial communities further. Recent advances in next-generation sequencing (NGS) technology have progressed our understanding of microbial communities associated with grapes and fermentations. We now have a finer appreciation of microbial diversity across wine producing regions to begin to understand how diversity can contribute to wine quality and style characteristics. In this review, we highlight literature surrounding wine-related microorganisms and how these affect factors interact with and shape microbial communities and contribute to wine quality. By discussing the geography, climate and soil of environments and viticulture and winemaking practices, we claim microbial biogeography as a new perspective to impact wine quality and regionality. Depending on geospatial scales, habitats, and taxa, the microbial community respond to local conditions. We discuss the effect of a changing climate on local conditions and how this may alter microbial diversity and thus wine style. With increasing understanding of microbial diversity and their effects on wine fermentation, wine production can be optimised with enhancing the expression of regional characteristics by understanding and managing the microbes present.
Human intestinal epithelial organoids (IEOs) are increasingly being recognised as a highly promising translational research tool. However, our understanding of their epigenetic molecular ...characteristics and behaviour in culture remains limited.
We performed genome-wide DNA methylation and transcriptomic profiling of human IEOs derived from paediatric/adult and fetal small and large bowel as well as matching purified human gut epithelium. Furthermore, organoids were subjected to in vitro differentiation and genome editing using CRISPR/Cas9 technology.
We discovered stable epigenetic signatures which define regional differences in gut epithelial function, including induction of segment-specific genes during cellular differentiation. Established DNA methylation profiles were independent of cellular environment since organoids retained their regional DNA methylation over prolonged culture periods. In contrast to paediatric and adult organoids, fetal gut-derived organoids showed distinct dynamic changes of DNA methylation and gene expression in culture, indicative of an in vitro maturation. By applying CRISPR/Cas9 genome editing to fetal organoids, we demonstrate that this process is partly regulated by TET1, an enzyme involved in the DNA demethylation process. Lastly, generating IEOs from a child diagnosed with gastric heterotopia revealed persistent and distinct disease-associated DNA methylation differences, highlighting the use of organoids as disease-specific research models.
Our study demonstrates striking similarities of epigenetic signatures in mucosa-derived IEOs with matching primary epithelium. Moreover, these results suggest that intestinal stem cell-intrinsic DNA methylation patterns establish and maintain regional gut specification and are involved in early epithelial development and disease.
The embryonic mouse lung is a widely used substitute for human lung development. For example, attempts to differentiate human pluripotent stem cells to lung epithelium rely on passing through ...progenitor states that have only been described in mouse. The tip epithelium of the branching mouse lung is a multipotent progenitor pool that self-renews and produces differentiating descendants. We hypothesized that the human distal tip epithelium is an analogous progenitor population and tested this by examining morphology, gene expression and in vitro self-renewal and differentiation capacity of human tips. These experiments confirm that human and mouse tips are analogous and identify signalling pathways that are sufficient for long-term self-renewal of human tips as differentiation-competent organoids. Moreover, we identify mouse-human differences, including markers that define progenitor states and signalling requirements for long-term self-renewal. Our organoid system provides a genetically-tractable tool that will allow these human-specific features of lung development to be investigated.
Filamentous growth in
is a stress response commonly induced under nutrient deprivation and by certain alcohols. It is a compound phenotype characterized by pseudohyphal growth, invasion and a shift ...to more polarized budding. Previous methods have not allowed the time-resolved determination of filamentous growth. Here we present a new method for budding pattern characterization that enables the measurement of filamentous growth and metabolite concentration during yeast cell growth at precise time intervals. By combining chemical cell immobilization and single-cell imaging using an oCelloScope™, this method provides more accurate budding pattern classification compared with previous methods. The applications of the method include, for example, investigation of quorum sensing-controlled yeast filamentous growth and metabolism under stress and identification of toxic metabolites.
An accurate method for yeast budding pattern determination is presented using a combination of oCelloScope™ imaging, chemical cell immobilization and proton (
H) NMR analysis. This new method furthermore enables the measurement of time-resolved metabolite concentration in parallel with monitoring yeast budding patterns.
The flavors of fermented plant foods and beverages are formed by microorganisms, and in the case of wine, the location and environmental features of the vineyard site also imprint the wine with ...distinctive aromas and flavors. Microbial growth and metabolism play an integral role in wine production, by influencing grapevine health, wine fermentation, and the flavor, aroma, and quality of finished wines. The contributions by which microbial distribution patterns drive wine metabolites are unclear, and while flavor has been correlated with fungal and bacterial composition for wine, bacterial activity provides fewer sensorially active biochemical conversions than fungi in wine fermentation. Here, we collected samples across six distinct wine-growing areas in southern Australia to investigate regional distribution patterns of fungi and bacteria and the association with wine chemical composition. Results show that both soil and must microbiota distinguish wine-growing regions. We found a relationship between microbial and wine metabolic profiles under different environmental conditions, in particular measures of soil properties and weather. Fungal communities are associated with wine regional distinctiveness. We found that the soil microbiome is a source of grape- and must-associated fungi and suggest that weather and soil could influence wine characteristics via the soil fungal community. Our report describes a comprehensive scenario of wine microbial biogeography where microbial diversity responds to the surrounding environment and correlates with wine composition and regional characteristics. These findings provide perspectives for thoughtful human practices to optimize food composition through understanding fungal activity and abundance. IMPORTANCE The composition of soil has long been thought to provide wine with characteristic regional flavors. Here, we show that for vineyards in southern Australia, the soil fungal communities are of primary importance for the aromas found in wines. We propose a mechanism by which fungi can move from the soil through the vine.
Polyphenols are naturally occurring compounds found largely in fruits and vegetables. The antioxidant properties of these polyphenols including total phenolic content (TPC), total flavonoid content ...(TFC), tannin content, 1,1-diphenyl-2-picrylhydrazyl free radical (DPPH), 2,2′-azinobis-(3-ethylbenzo-thiazoline-6-sulfonic acid) (ABTS) scavenging abilities and ferric ion reducing antioxidant power (FRAP) were measured among sixteen (16) plant foods (mango, blueberry, strawberry, black carrot, raspberry, dark grapes, garlic, ginger, onion, cherry, plum, apple, papaya, peach, pear and apricot) by modifying, standardising and translating existing antioxidant methods using a 96-well plate reader. Eighteen targeted phenolic acids and flavonoids were characterised and quantified using high-performance liquid chromatography-photometric diode array (HPLC-PDA) and verified by modifying an existing method of liquid chromatography coupled with electrospray-ionisation triple quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF/MS). While most of these compounds were accurately detected by the HPLC-PDA at a low concentration, a few polyphenols in low concentrations could be only be characterised using the LC-ESI-QTOF/MS method. Our results showed that mango possessed the highest overall antioxidant activity, phenolic acid and flavonoid content among the selected fruits. Factor analysis (FA) and Pearson’s correlation tests showed high correlations among ABTS, DPPH, FRAP and phenolic acids, implying the comparable capabilities of scavenging the DPPH/ABTS free radicals and reducing ferric ions from the antioxidant compounds in the samples. Phenolic acids contributed significantly to the antioxidant activities, and flavonoids contributed more to tannin content based on the correlations. Overall, methods modified and standardized in this study can provide better understanding of high throughput technologies and increase the reliability of antioxidant data of different plant foods.
Saccharomyces cerevisiae can alter its morphology to a filamentous form associated with unipolar budding in response to environmental stressors. Induction of filamentous growth is suggested under ...nitrogen deficiency in response to alcoholic signalling molecules through quorum sensing. To investigate this further, we analysed the budding pattern of S. cerevisiae cells over time under low nitrogen conditions while concurrently measuring cell density and extracellular metabolite concentration. We found that the proportion of cells displaying unipolar budding increased between local cell densities of 4.8 × 10
and 5.3 × 10
cells/ml. This increase in unipolar budding was not reproduced with cells growing at the critical cell density and in conditioned media. Growth under high nitrogen conditions also resulted in increased unipolar budding between local cell densities of 5.2 × 10
and 8.2 × 10
cells/ml, but with differences in metabolite concentration compared to low nitrogen conditions. Neither cell density, metabolite concentration, nor nitrogen deficiency were therefore sufficient to increase unipolar budding. Therefore, by using the budding pattern as an early indicator of filamentous growth, our results suggest that quorum sensing may not control the switch of budding behaviour in S. cerevisiae. Only a high concentration of the putative signalling molecule, 2-phenylethanol, resulted in an increase in unipolar budding. However, this concentration was not physiologically relevant, suggesting toxicity rather than a known quorum sensing mechanism.
This study characterizes the environmental factors driving rotundone concentrations in grape berries by quantifying rotundone variability and correlating it with viticultural parameters. Dissection ...of the vineyard into distinct zones (on the basis of vigor, electrical soil conductivity, and slope), vine into orientations to sun (shaded/unshaded), and grape bunches into sectors (upper and lower and front and back) shows the influence of vine vigor, sunlight, and temperature. Occurrence of the highest rotundone concentration was observed in shaded bunch sectors and vines and from higher vigor vines in the southern-facing areas of the vineyard. The highest concentration of rotundone is consistently found at the top and in shaded sectors of bunches, and this correlates to lower grape surface temperatures. Modeling showed that berry temperature exceeding 25 °C negatively affects the rotundone concentration in Shiraz. Both natural and artificial shading modulated the grape surface and air temperature at the bunch zone and increased the rotundone concentration, without affecting other grape berry quality parameters. Thus, temperature and possibly sunlight interception are the main determinants of rotundone in grape berries. Vineyard topography, vine vigor, vine row, and grape bunch orientation influence the level of berry shading and can, therefore, adjust bunch surface and zone temperatures and influence the berry rotundone concentration.
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