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…

Moscatel vine-shoot extracts as grapevine biostimulant to increase the varietal aroma of Airén wines

There is a growing interest in the exploitation of vine-shoots waste, since they are often left or burned. Sánchez-Gómez et al. [1] have shown that vines-shoots aqueous extracts have significant contents of bioactive compounds, among which several polyphenols and volatiles are highlighted. Recent studied had demonstrated that the chemical composition of vine-shoots is enhanced when vine-shoots are toasted
[2,3]. The application of vegetable products in the vineyards has led to significant changes towards a more “Sustainable Viticulture”. An innovative foliar application for Airén vine-shoot extracts have been carried out to the vineyard. It has been shown that they act as grape biostimulants, improving certain wine quality characteristics [4].

Use of chitosan as a secondary antioxidant in juices and wines

Chitosan is a polysaccharide produced from the deacetylation of chitin extracted from crustaceous and fungi. In winemaking chitosan is mainly used in the clarification of grape juice and wine, stabilization of white wines, removal of metals and to prevent wine spoilage by undesired microorganisms. The addition of chitosan to model wine systems was able to retard browning, reduce levels of metallic ions (Fe and Cu) and to protect varietal thiols due to its antiradical activity1. The present experiment was planned in order to evaluate the use of chitosan as a secondary antioxidant at three different stages of Sauvignon blanc fermentation and winemaking. Sauvignon blanc juices from three different locations were obtained at a commercial winery in Marlborough, New Zealand. One lots of grapes was collected from a receival bin and pressed into juice with a water-bag press, and a further juice sample was collected from a commercial pressing operation. Chitosan (1 g/L, low molecular weight, 75 – 85% deacetylated) was added to the juice after pressing, after cold settling, after fermentation, or at all these stages. Controls without any chitosan additions were also prepared.

Towards multi-purpose valorisation of polyphenols from grape pomace: Pressurized liquid extraction coupled to purification by membrane processes

Grape by-products (including skins, seeds, stems and vine shoots) are rich in health promoting polyphenols. Their extraction from winery waste and their following purification are of special interest to produce extracts with high added value compounds. Meanwhile, the growing concern over environmental problems associated with economic constraints, require the development of environmentally sustainable extraction technologies. The extraction using semi-continuous subcritical water, as a natural solvent at high temperature and high pressure a technology is promising “green” technology that is environmentally friendly, energy efficient and improve the extraction process in plant tissues.

Light-struck taste in white wine: enological approach for its prevention

Light-struck taste is a defect prevalent in white wines bottled in clear glass light-exposed for a considerable amount of time leading to a loss of color and appearance of sulfur-like odors. The reaction involves riboflavin (RF), a highly photosensitive compound that undergoes to intermolecular photoreduction by the uptake of two electron equivalents from an external donor, the methionine. The reaction includes different steps forming methional which is extremely unstable and decomposes to methane thiol and acrolein. The reaction of two molecules of methane thiol yields dimethyl disulfide. Methane thiol is highly volatile, has a low perception threshold (2 to 10 µg/L in wine) and confers aroma-like rotten eggs or cabbage.

Study of the colour and phenolic evolution of three different tannin/anthocyanin ratios over time in a model wine

Phenolic compounds are important quality indicators in red wine. A large number of polyphenols play an important role in wine development, contributing to the colour and the sensory perception of the wines. Anthocyanins are the pigments responsible for the colour in young red wines while tannins are the principal contributors to the bitterness and the astringency of the wines. Wine polyphenols are considered more complex molecules than grape phenolics, due to the enormous number of chemical reactions which take place during the entire winemaking process and storage, forming more stable compounds.