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…

IBMP-Polypenol interactions: Impact on volatility and sensory perception in model wine solution

3-Isobutyl-2-methoxypyrazine (IBMP) is one of the key molecules in wine aroma with a bell pepper aroma and a very low threshold in wine, 1-6 ng/L for white wine and 10-16 ng/L in red wine1. The differences in these thresholds are likely due to IBMP-non volatile matrix interactions. It has indeed been shown that polyphenols may influence the volatility of flavor compounds2. In the present study, we focus on IBMP-polyphenols interactions in relation to volatility and sensory perception in model wine solution. Methods: 1. GC-MS Static Headspace Analysis: Samples were analyzed by Static headspace analysis with an Agilent 7890A gas chromatograph coupled to HP 5975C mass spectrometry detector (Agilent Technologies, Santa Clara, CA, USA).

Effects of post-fermentative cold maceration on chemical and sensory characteristics of Syrah, Cabernet Franc and Montepulciano wines

Astringency sensation decreases slowly during the aging of red wine. Complex reactions of condensation and precipitation of wine polyphenols are involved in this phenomenon. Wine composition and conditions of aging, such as temperature and oxygen availability, strongly influence evolution of the phenol matrix. Recently, a Post-Fermentative cold Maceration (PFM) technique was tested with the aim of accelerating reactions leading to the reduction of astringency and exploiting chemical compounds not extracted from the solid parts of grapes during the previous traditional maceration phase. To this purpose, an innovative maceration system was engineered and used to perform PFM trials on marc derived from vinification of different varieties of red grapes.

Determination of metallic elements in Chilean wines by atomic absorption spectroscopy and inductively coupled plasma–mass spectrometry

The chemical composition of wines depends on series of variables such as the type of grape, edaphoclimatic conditions, and viticulture and winemaking practices employed during production. Metallic elements play a significant role during winemaking (e.g. as catalysts of oxidation reactions) and have been previously employed for the classification of wines according to provenance. In this work, we focused on the analysis of metallic elements (K, Na, Ca, Zn, Cu, Fe, Mg, Mn, Ni, Cr, Al, Pb, Cd, Hg, Se, Co, Sn and As) in 145 Chilean wine samples (102 reds and 43 white wines), of seven grape varieties, and five of the major wine producing regions in Chile.

Effect of the winemaking technology on the phenolic compounds, foam parameters in sparklig wines

Contribution Sparkling wines elaborated following the traditional method undergo a second fermentation in closed bottles of base wines, followed by aging of wines with lees for at least 9 months. Most of the sparkling wines elaborated are white and rosé ones, although the production of red ones is highly increasing. One of the initial problems in red sparkling wine processing is to obtain suitable base wines that should have moderate alcohol content and astringency and adequate color intensity; which is difficult to obtain when grapes must be harvested at low phenolic and industrial maturity stage. The low phenolic maturity degree in the red grapes makes essential to choose an adequate winemaking methodology to obtain the base wines because the extracted polyphenols will vary according the winemaking technique: carbonic maceration or destemmed-crushed grapes.

Analysis of voltammetric fingerprints of different white grape musts reveals genotype-related oxidation patterns

Must oxidation is a complex process involving multiple enzymatic transformations, including the oxidation of phenolics containing an ortho-diphenol function. The latter process has a primary influence on wine aroma characteristics and stability, due to the central role of ortho-diphenols in the non-enzymatic oxidative reactions taking place during winemaking and in finished wine. Although oxidation of must is traditionally avoided, in recent years its contribution to wine quality has been revisited, and in some cases improvements to wine aroma have been observed with the application of controlled must oxidation. Nowadays there is a great interest in the wine industry towards the identification of specific markers or patterns to characterize and classify the response of grape must to oxidation.