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…

Interest and impact of PVP/PVI (Polyvinylpyrrolidone/ Polyvinylimidazole) on winemaking and final quality of wines

Céline Sparrow a, Christophe Morge a, a SOFRALAB SAS, 79, av. A.A. Thévenet – CS 11031 – 51530 Magenta, France Consumers’ health and security force authorities to limit, in wine as in others food industry products, the concentration in « dangerous » molecules. Therefore the legal limit in heavy metals keeps on decreasing. As per proof EU regulation just decrease the stain concentration in wine from 0,2 to 0,15 mg/l. Certain changes , such as sodium arsenite treatment in vines, disappearance of brass in wineries to the benefit of stainless steel, limit even more the concentration of heavy metals in wines. But the use of copper derivates in vines treatments is difficult to replace. In the case of wine and its elaboration, the problem is even more complex. Indeed, regulation forces the wine producers to control the concentration of certain heavy metals in final wines.

On the losses of dissolved CO2 during champagne aging

A misconception lingers in the minds of some wine consumers that Champagne wines don’t age. It’s largely a myth, certainly as far as the best cuvees are concerned. Actually, during the so-called autolysis period of time (in the closed bottle, after the “prise de mousse”), complex chemical reactions take place when the wine remains in contact with the dead yeast cells, which progressively bring complex and very much sought-after aromas to champagne. Nevertheless, despite their remarkable impermeability to liquid and air, caps or natural cork stoppers used to cork the bottles are not 100% hermetic with regard to gas transfers. Gas species therefore very slowly diffuse through the cap or cork stopper, along their respective inverse partial pressure. After the “prise de mousse”, because the partial pressure of CO2 in the bottleneck reaches up to 6 bars (at 12 °C), gaseous CO2 progressively diffuse from the bottle to the ambient air
(where the partial pressure of gaseous CO2 is only of order of 0,0004 bar).

Grape metabolites, aroma precursors and the complexities of wine flavour

A critical aspect of wine quality from a consumer perspective is the overall impression of wine flavour, which is formed by the interplay of volatile aroma compounds, their precursors, and taste and matrix components. Grapes contribute some potent aroma compounds, together with a large pool of non-volatile precursors (e.g. glycoconjugates and amino acid conjugates). Aroma precursors can break down through chemical hydrolysis reactions, or through the action of yeast or enzymes, significantly changing the aroma profile of a wine during winemaking and storage. In addition, glycoconjugates of monoterpenes, norisoprenoids and volatile phenols, together with sulfur-conjugates in wine, provide a reservoir of additional flavour through the in-mouth release of volatiles which may be perceived retro-nasally.

Characterization of commercial enological tannins and its effect on human saliva diffusion

Commercial oenological tannins (TECs) are widely used in the wine industry. TECs are rich in condensed tannins, hydrolyzable tannins or a mixture of both. Wine grapes are a important source of proanthocyanidins or condensed tannins while oak wood possess a high concentration of hydrolyzable tannins (Obreque-Slier et al., 2009). TECs contribute with the antioxidant capacity of wine, catalyze oxide-reduction reactions and participate in the removal of sulfur compounds and metals.

Effect of concentration and competition between different fungicide residues on the adsorption efficiency of activated vegetal fibres for treatment of wine

Vineyards are strongly exposed to fungal diseases, attacks from insects and competition with weeds. Most treatments used on grape vines contain synthetic active substances, which may be transferred to the wine. Such pesticides have a negative image because many active substances are potential health hazards. A specific oenological treatment allowing the reduction of pesticide residues in wine based on activated vegetable fibres (AVF) is under examination by the International Organisation for Vine and Wine. This technique works efficiently and alters the wine only little (Lempereur et al. 2014).