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…

The influence of soil management practices on functional traits and biodiversity of weed communities in Swiss vineyards

Green cover in vine rows provides many ecological services, but can also negatively impact the crop, depending on the weed species. The composition of a vineyard weed community is influenced by many parameters. Ensuring an evolution of the vine row flora into a desired direction is therefore very complex. A key step towards this goal is to know which factors influence the establishment of the weed community and which types of communities are best suited for vineyards. In this study, we analysed the weed communities of several vineyards in the Lake Geneva region (379 botanical surveys on 117 plots), with the aim to highlight the links between soil management practices (chemical and mechanical weeding, mowing, mulching roll) and phytosociological profiles, biodiversity and selected functional traits (growth forms, life strategies, root depth). T

To a better understanding of the impact of vine nitrogen status on volatile thiols from plot to transcriptome level

Volatile thiols contribute largely to the organoleptic characteristics and typicity of Sauvignon blanc wines. Among this family of odorous compounds, 3-sulfanylhexan-1-ol (3SH) and 4-methyl-4-sulfanylpentan-2-one (4MSP) have a major impact on wine flavor. These thiols are formed during alcoholic fermentation by the yeast from odorless and non-volatile precursors found in the berry and the must. The effect of vine nitrogen status on 3SH and 4MSP in Sauvignon blanc wine and on the glutathionylated and cysteinylated precursors of 3SH (Glut-3SH and Cys-3SH) was investigated in this study.

Effects of bottle closure type on sensory characteristics of Chasselas wines

Several winemaking operations, such as filtration, pumping, and racking, are known to potentially facilitate the incorporation of atmospheric O2 into the wine. Control of grape must oxidation is one key aspect in the management of white wine aroma expression, color stability and shelf-life extension. On the one hand, controlled must oxidation may help to remove highly reactive phenolic compounds, which otherwise could contribute to premature oxidation. And on the other hand, in certain cases of extreme protection of the must from O2 (e.g. pressing under inert atmosphere), it can help to preserve varietal aromas and natural must antioxidants.

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.

How do different oak treatment affect the sensory composition of Chenin blanc wines over time?

Wooden barrels have been the preferred method for oak maturation for wines, but the use of alternative oak products, such as staves and oak chips have increased in South Africa due to lower production costs. This study investigated the effect of different oak products used during fermentation and ageing on the sensory profile, degree of liking and perceived quality of a South African Chenin blanc wine. The different wine treatments included an unoaked tank control wine, wines matured in 5th fill barrels, wines matured in new barrels from three different cooperages, and wines matured in 5th fill barrels with stave inserts from two different cooperages.