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…

New molecular evidence of wine yeast-bacteria interaction unraveled by untargeted metabolomic profiling

Bacterial malolactic fermentation (MLF) has a considerable impact on wine quality. The yeast strain used for primary fermentation can consistently stimulate (MLF+ phenotype) or inhibit (MLF- phenotype) malolactic bacteria and the MLF process as a function of numerous winemaking practices, but the molecular evidence behind still remains a mystery. In this study, such evidence was elucidated by the direct comparison of extracellular metabolic profiles of MLF+ and MLF- yeast phenotypes. Untargeted metabolomics combining ultrahigh-resolution FT-ICR-MS analysis, powerful machine learning methods and a comprehensive wine metabolite database, discovered around 800 putative biomarkers and 2500 unknown masses involved in phenotypic distinction.

Effects of a new vacuum evaporation method on chemical and sensory properties of must and wine

A new process for vacuum evaporation was developed where evaporation takes place near the inner surface of a vortex produced by a rotor submerged in the liquid. Contrary to the state of the art the Vortex rotor process does not need a vacuum vessel but the rotating liquid creates a geometrically stable low pressure void surrounded by a vortex stabilized by the equilibrium between centrifugal forces and the pressure difference. First tests with water and sugar solutions at concentrations similar to grape must were conducted to verify the theoretical predictions, test the performance under different conditions and study the effect of various process parameters (Rösti et al 2015).

Development and validation of a standardized oxidation assay for the accurate measurement of the ability of different wines to form “de novo” oxidation-related aldehydes

From the standpoint of wine aroma oxidation there are two effects observed: aroma degradation of oxygen sensitive compounds (polyfunctional mercaptans) and the appearance of new substances with high aromatic power (acetaldehyde, methional, phenylacetaldehyde, sotolon, alkenals, isobutanal and 2, 3-metylbutanals) (1-5). According to our experience, Strecker aldehydes are compounds with highest sensory relevance in the oxidative degradation of many wines (5-7).

Glutathione content evolution during spontaneous alcoholic fermentations of Sangiovese grapes

Glutathione is a tripeptide (γ-Glu-Cys-Gly), which can occur in grapes, in must and in wine prevalently in the reduced form as well as in the oxidized form as glutathione disulfide. The importance of the reduced form of glutathione lies in its antioxidant activity. In must, it limits browning by reducing o-quinones produced by polyphenol oxidase activity on hydroxycinnamic acids; in wine, it exerts a protective effect on various aromatic compounds. Glutathione concentration in wine is lower than in grape juice and variable as it depends on several factors, ranging from the native content of grapes to winemaking technique.

Improving the phenolic composition of cv tempranillo wines by blending grapes of different ripening state

The aim of this work was to reduce the alcohol content of Tempranillo wine. Tempranillo wines were produced by grapes harvested at different ripening dates (August 11 which was 21 oBrix and September 28 with 25 oBrix). At the second date, the Tempranillo wines were elaborated as follows: grapes were destemmed, crushed and collected into 50 L stainless-steel vats. Before preferementative maceration in cold, 50 % (M1) and 70 % (M2) of the must have been replaced by the same percentage of must from the first harvest. In addition, a control wine (C) was performed with only grapes from the second harvest.