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…

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

Contribution of Piperitone to the mint nuances perceived in the aging bouquet of red Bordeaux wines

During the tasting of a fine, old wine, the aromas generated in the glass are intertwined in an intimate, complex manner, expressing the fragrance of the aging bouquet. This aging bouquet, which develops during bottle storage through a complex transformation process, may result in a broad palette of nuances. Among these, undergrowth, truffle, toasted, spicy, licorice, fresh red- and black-berry fruit and mint descriptors were recently identified as features of its olfactory representation for red Bordeaux wines. Although a targeted chemical approach focusing on volatile sulfur compounds revealed the role played by dimethyl sulfide, 2-furanmethanethiol, and 3-sulfanylhexanol as molecular markers of the typicality of the wine aging bouquet of red Bordeaux wines, its chemical transcription has only partially been elucidated.

Proteomic and activity characterization of exocellular laccases from three Botrytis cinerea strains

Botrytis cinerea is a fungus that causes common infection in grapes and other fruits. In winemaking, its presence can be both considered desirable in the case of noble rot infection or undesirable when grey rot is developed. This fungus produces an extracellular enzyme known as laccase which is able to cause oxidation of phenolic compounds present in must and wine, causing most of the times a decrease in its quality and problems during the winemaking process [1]. Material and methods: Three B. cinerea strains (B0510, VA612 and RM344) were selected and grown in a liquid medium adapted from one previously described [2]. The enzyme was isolated by tangential ultrafiltration of the culture medium using a QuixStand system equipped with a 30 KDa filtration membrane.

Impact of varying ethanol and carbonation levels on the odor threshold of 1,1,6-trimethyl-1,2-dihydronaphtalene (petrol off-flavor) and role of berry size and Riesling clones

1,1,6-trimethyl-1,2-dihydronaphtelene (TDN) evokes the odor of “petrol” in wine, especially in the variety Riesling. Increasing UV-radiation due to climate change intensifies formation of carotenoids in the berry skins and an increase of TDN-precursors1. Exploring new viticultural and oenological strategies to limit TDN formation in the future requires precise knowledge of TDN thresholds in different matrices. Thresholds reported in the literature vary substantially between 2 µg/L up to 20 µg/L2,3,4 due to the use of different methods. As Riesling grapes are used for very different wine styles such as dry, sweet or sparkling wines, it is essential to study the impact of varying ethanol and carbonation levels.

Evaluation of Polarized Projective Mapping as a possible tool for attributing South African Chenin blanc dry wine styles

Multiple Factor Analysis (MFA) According to the Chenin blanc Association of South Africa, there are three recognized dry wine styles, Fresh and Fruity (FF), Rich and Ripe Unwooded (RRU), and Rich and Ripe Wooded (RRW), classically attributed with the help of sensory evaluation. One of the “rapid methods” has drawn our attention for the purpose of simplifying and making style attribution for large sample sets, evaluated during different sessions, more robust. Polarized Projective Mapping (PPM) is a hybrid of Projective Mapping (PM) and Polarised Sensory Positioning (PSP). It is a reference-based method in which poles
(references) are used for the evaluation of similarities and dissimilarities between samples.