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…

Effect of malolactic fermentation in barrels or stainless steel tanks on wine composition. Influence of the barrel toasting

Ellagitannin, anthocyanin and woody volatile composition of Cabernet Sauvignon wines aged in oak barrels for 12 months was evaluated. Depending on the container where malolactic fermentation (MLF) was carried out, two wine modalities were investigated: wines with MLF carried out in stainless steel tanks and barrel-fermented wines. Three toasting methods (medium toast, MT; medium toast with watering, MTAA; noisette) were considered for ageing of each wine modality. Sensory analyses (triangle and rating tests) were also performed. Two-way ANOVA of the raw experimental data revealed that the toasting method and the container where MLF took place, as well as the interaction between both factors, have a significant influence (p < 0.05) on ellagitannin, anthocyanin and woody volatile profiles of Cabernet Sauvignon wines.

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.

An excessive leaf-fruit ratio reduces the yeast assimilable nitrogen in the must

Yeast assimilable nitrogen (YAN) in the grape must is a key variable for wine quality as a source of aroma precursors. In a situation of YAN deficiency, a foliar urea application upon the vine at veraison enhances YAN concentration and facilitates must fermentation. In 2013, Agroscope investigated the impact of leaf-fruit ratio on the nitrogen (N) assimilation and partitioning in grapevine Vitis vinifera cv. Chasselas following foliar-urea application with the aim of improving its efficiency on the YAN concentration.

Screening sensory-directed methodology for the selection of non-saccharomyces wine yeasts based on perceived aroma quality

The present work contributes by developing a rapid sensory-directed methodology for the screening and selection of high quality wines with different sensory profiles Therefore, Verdejo and Tempranillo musts were fermented with 50 different yeasts each under controlled laboratory conditions. Resulting samples were firstly categorized according to five levels of quality by a panel of wine professionals (Sáenz-Navajas, Ballester et al. 2013). Higher quality samples were described by flash profiling by a semi-trained panel
(Valentin, Chollet et al. 2012) and most distinctive samples were screened by gas chromatography-olfactometry (GC-O) (López, Aznar et al. 2002).

Prediction of the production kinetics of the main fermentative aromas in alcoholic fermentation

Fermentative aromas (especially esters and higher alcohols) highly impact the organoleptic profile of young and white wines. The production of these volatile compounds depends mainly on temperature and Yeast Available Nitrogen (YAN) content in the must. Available dynamic models predict the main reaction
(bioconversion of sugar into ethanol and CO2 production) but none of them considers the production kinetics of fermentative aroma compounds during the process of fermentation. We determined the production kinetics of the main esters and higher alcohols for different values of initial YAN content and temperature, using an innovative online monitoring Gas Chromatography device.