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…

Novel contribution to the study of mouth-feel properties in wines

In general, there is a well-established lexicon related to wine aroma and taste properties; however mouth-feel-related vocabulary usually includes heterogeneous, multimodal and personalized terms. Gawel et al.
(2000) published a wheel related to mouthfeel properties of red wine. However, its use in scientific publications has been limited. The authors accepted that the approach had certain limitations as it included redundant and terms with hedonic tone and some others were absent. It is of high interest to generate a mouth-feel lexicon and finding the chemical compound or group of compounds responsible for such properties in red wine. In the present work a chemical fractionation method has been developed.

Impact of non-fruity compounds on red wines fruity aromatic expression: the role of higher alcohols

A part, at least, of the fruity aroma of red wines is the consequence of perceptive interactions between various aromatic compounds, particularly ethyl esters and acetates, which may contribute to the perception of fruity aromas, specifically thanks to synergistic effects.1,2 The question of the indirect impact of non-fruity compounds on this particular aromatic expression has not yet been widely investigated. Among these compounds higher alcohols (HA) represent the main group, from a quantitative standpoint, of volatiles in many alcoholic beverages. Moreover, some bibliographic data suggested their contribution to the aromatic complexity by either increasing or masking flavors of wine, depending of their concentrations.

Effect of mixed Torulaspora delbrueckii-Saccharomyces cerevisiae culture on rose quality wine

Alcoholic fermentation using no Saccharomyces wine is an effective means of modulating wine aroma. This study investigated the impact of coinoculating Torulaspora delbruecki with two Saccharomyces cerevisiae commercial yeast (QA23, Lallemand; Red Fruit, Sepsa-Enartis) on enological quality parameters, volatile composition and sensory analysis. The following assays were performed on Tempranillo variety: Saccharomyces QA23 (CTQA), Saccharomyces Red Fruit (CTRF), coinoculated T. delbrueckii + S.cerevisiae QA23 (CIQA) and coinoculated T. delbrueckii + S.cerevisiae (CIRF).

Measurements of the oxygen dissolved in white wines elaborated in barrels without to open the bung of the barrels

Bases on oxoluminescence, we have developed an innovative device for measuring dissolved oxygen in wines in barrels without opening the bung. This system is directly inserted into the wood during the barrel elaboration and can be positioned at different locations of the barrel (the head, the hull …). During two successive vintages we have used this device notably to follow the oxygen dissolved of whites wines elaborated in barrels. This allowed us initially to monitor the oxygen levels of the harvest to bottling the whole elaboration process in barrels of white wines without using techniques of measurement suitable to modify the real values in wines (opening the bung to plunge an oximeter).

Crown procyanidin: a new procyanidin sub-family with unusual cyclic skeleton in wine

Condensed tannins (also called proanthocyanidins) are a widely distributed throughout in plants kingdom and are one of the most important classes of secondary metabolites, in addition, they are part of the human diet. In wine, they are extracted during the winemaking process from grape skins and seeds. These compounds play an important role in red wine organoleptic characteristics such as color, bitterness and astringency. Condensed tannins in red wine are oligomers and polymers of flavan-3-ols unit such as catechin, epicatechin, epigallocatechin and epicatechin-3-O-gallate. The monomeric units can be linked among them with direct interflavanoid linkage or mediated by aldehydes.