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…

Glutathione content evolution during spontaneous alcoholic fermentations of Sangiovese grapes

Glutathione is a tripeptide (γ-Glu-Cys-Gly), which can occur in grapes, in must and in wine prevalently in the reduced form as well as in the oxidized form as glutathione disulfide. The importance of the reduced form of glutathione lies in its antioxidant activity. In must, it limits browning by reducing o-quinones produced by polyphenol oxidase activity on hydroxycinnamic acids; in wine, it exerts a protective effect on various aromatic compounds. Glutathione concentration in wine is lower than in grape juice and variable as it depends on several factors, ranging from the native content of grapes to winemaking technique.

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.

Impact of glutathione and elemental sulphur juice addition on the volatile thiol production in South African Sauvignon blanc wine

Three compounds, 3-mercaptohexanol (3MH), 3-mercaptohexyl-acetate (3MHA) and 4-mercapto-4-methylpentan-2-one (4MMP), also known as varietal thiols, have been identified to contribute positively to wine aroma and are responsible for the distinct gooseberry, grapefruit, guava and box tree character found in Sauvignon blanc wines. Certain volatile thiol compounds though, can cause off-aromas of onion, garlic, rubber and rotten egg, this group of molecules is known as reductive sulphur compounds (RSC). This study looks into how the addition of sulphur-compounds to Sauvignon blanc juice contributes to the varietal thiol (3MH and 3MHA) concentration and reductive sulphur compound concentration in South African Sauvignon blanc wine.

Quantification of the production of hydrogen peroxide H2O2 during wine oxidation

Chemical studies aiming at assessing how a wine reacts towards oxidation usually focus on the characterization of wine constituents, such as polyphenols, or oxidation products. As an alternative, the key oxidation intermediate hydrogen peroxide H2O2 has never been quantified, although it plays a pivotal role in wine oxidation. H2O2 is obtained from molecular oxygen as the result of a first cascade of oxidation reactions involving metal ions and polyphenols. The produced H2O2 then reacts in a second cascade of oxidation to produce reactive hydroxyl radicals that can attack almost any chemical substrate in wine.

Update knowledge about the presence of condensed tannins in grapes and their contributions to astringency perception

Condensed tannin is a principle group of polyphenol compounds derived from grape, greatly contributing to the bioactivity and the sensory perception of wine. Condensed tannins present as a heterogeneous mixture in nature involving various degrees of both polymerization and galloylation. Even though multiple attempts focusing on fractionation of grape condensed tannins by solid-phase have been conducted over the past decades, few individual tannins have been purified and identified. Hence, our knowledge on grape and wine condensed tannin moleculars has to be limited at the several known monomeric, dimeric and trimeric proanthocyanidins