Macrowine 2021
IVES 9 IVES Conference Series 9 Capture depletion of grapevine DNA: an approach to advance the study of microbial community in wine

Capture depletion of grapevine DNA: an approach to advance the study of microbial community in wine

Abstract

The use of next-generation sequencing (NGS) has helped understand microbial genetics in oenology. Current studies mainly focus on barcoded amplicon NGS but not shotgun sequencing, which is useful for functional analyses. Since the high percentage of grapevine DNA conceals the microbial DNA in must, the majority of sequencing data is wasted in bioinformatic analyses. Here we present capture depletion of grapevine whole genome DNA. By using biotinylated RNA baits made from genomic grapevine libraries, the grapevine DNA is hybridized to the baits and captured by magnetic beads while the targeted microbial DNA is left and subsequently sequenced. A pilot study was carried out to mimic degraded complex materials. Using known complex microbial samples and spiking in large portion of grapevine DNA, the hybridization and depletion took place with quantification by qPCR. Different parameters, such as hybridization hours, temperatures and bait amounts were also tested for potential effects. The aim is to provide an insight into depletion of undesired grapevine DNA and to enhance the data yield in NGS studies of microbial DNA with a more cost effective way suitable for future oenological studies.

Publication date: May 17, 2024

Issue: Macrowine 2016

Type: Poster

Authors

Sarah S.T. Mak*, Anders Hansen, Christian Carøe, Jacob Enk, Jean-Marie Rouillard, M Thomas P Gilbert

*Centre for GeoGenetics

Contact the author

Tags

IVES Conference Series | Macrowine | Macrowine 2016

Citation

Related articles…

Oenological features of Sangiovese wine from vinification of whole grape berries

The present study was performed in a traditional winery located in the viticultural area of Brunello di Montalcino, Siena, Italy, in the vintage 2015. Actually, in this winery Sangiovese grape musts are fermented in large oak barrels by a single strain of Saccharomyces cerevisiae previously isolated in the same winery. Pumping over operations are carried out once or twice a day until the end of alcoholic fermentations. The aim of this work was to investigate on the oenological properties of Sangiovese wine produced with the traditional winemaking process adopted by the winery under study obtained from the fermentation of whole berries compared to that from crushed grape must. In particular, two lots of 65q of Sangiovese grapes from the same 3ha vineyard were vinified in 150hL oak barrels.

Chemical markers in wine related to low levels of yeast available nitrogen in the grape

Nitrogen is an important nutrient of yeast and its low content in grape must is a major cause for sluggish fermentations. To prevent problems during fermentation, a supplementation of the must with ammonium salts or more complex nitrogen mixtures is practiced in the cellar. However this correction seems to improve only partially the quality of wine [1]. In fact, yeast is using nitrogen in many of its metabolic pathways and depending of the sort of the nitrogen source (ammonium or amino acids) it produces different flavor active compounds. A limitation in amino acids can lead to a change in the metabolic pathways of yeast and consequently alter wine quality.

The use of cation exchange resins for wine acidity adjustment: Optimization of the process and the effects on tartrate formation and oxidative stability

Acidity adjustments are key to microbial control, sensory quality and wine longevity. Acidification with cation exchange resins -in acid cycle- offers the possibility to reduce the pH by exchanging wine cations, such as potassium (K+), for hydrogen ions (H+). During the exchange process, the removal of potassium and calcium ions contributes to limiting the formation of tartrate salts, thus offering an alternative solution to conventional methods for tartrate stability. Moreover, the reduction of wine pH and the removal of metals catalyzers (e.g. iron) could positively impact the wine’s oxidative stability. Therefore, the aims of this work were (a) to optimize the ion exchange process by testing different volumes and concentrations of sulfuric acid (H2SO4) during the acid cycle, (b) evaluate the effects of the ion exchange process on the formation of tartrate salts, and (c) analyze the oxidative stability of the treated wines.

Microbial stabilization of wines using innovative coiled UV-C reactor process: impact on chemical and organoleptic proprieties

For several years, numerous studies aimed at limiting the use of SO2 in wines (thermal treatments, pulsed electric fields, microwaves …). Processes must be able to preserve the organoleptic qualities of wines with low energy consumption. In this context, ultraviolet radiations (UV-C), at 254 nm, are well known for their germicidal proprieties. In order to inactivate microorganisms in grape juice and wine without affecting the quality of the product, efficiency of UV-C treatment process should be optimized.

Petrolomics-derived data interpretation to study acetaldehyde-epicatechin condensation reactions

During red wine ageing or conservation, color and taste change and astringency tends to reduce. These changes result from reactions of flavan-3-ols and/or anthocyanins among which condensation reactions with acetaldehyde are particularly important. The full characterization of these reactions has not been fully achieved because of difficulties in extracting and separating the newly formed compounds directly from wine. Model solutions mimicking food products constitute a simplified medium for their exploration, allowing the detection of the newly formed compounds, their isolation, and their structure elucidation.