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…

Impact of smoke exposure on the chemical composition of grapes

Vineyard exposure to smoke can lead to grapes and wine which exhibit objectionable smoky and ashy aromas and flavours, more commonly known as ‘smoke taint’ [1, 2]. In the last decade, significant bushfires have occurred around the world, including near wine regions in Australia, Canada, South Africa and the USA, as a consequence of the warmer, drier conditions associated with climate change. Considerable research has subsequently been undertaken to determine the chemical, sensory and physiological consequences of grapevine exposure to smoke. The sensory attributes associated with smoke-tainted wine have been linked to the presence of several smoke-derived volatile phenols, such as guaiacols, syringols and cresols [2].

Modulating role of SO2 in white wine protein haze formation

Despite the extensive research performed during the last decades, the multifactorial mechanism responsible for the white wine protein haze formation is not fully characterized. Herein, a new model is proposed, which is based on the experimental identification of sulfur dioxide as a major modulating factor inducing wine protein haze upon heating. As opposed to other reducing agents, such as 2-mercaptoethanol, dithiothreitol and tris(2-carboxyethyl)phosphine hydrochloride (TCEP), the addition of SO2 to must/wine upon heating cleaves intraprotein disulfide bonds, hinders thiol-disulfide exchange during protein interactions and can lead to the formation of novel inter/intraprotein disulfide bonds. Those are eventually responsible for wine protein aggregation which follows a nucleation-growth kinetic model as shown by dynamic light scattering [1].

Supramolecular approaches to the study of the astringency elicited by wine phenolic compounds

The objective of this study is to review the scientific evidences and to advance into the knowledge of the molecular mechanisms of astringency. Astringency has been described as the drying, roughing and puckering sensation perceived when some food and beverages are tasted (1). The main, but possibly not the only, mechanism for the astringency is the precipitation of salivary proteins (2,3). Between phenolic compounds found in red wines, flavan-3-ols are the group usually related to the development of this sensation. Other compounds, phenolic or not, like anthocyanins, polysaccharides and mannoproteins could act modifying or modulating astringency perception by hindering the interaction between flavanols and salivary proteins either because of their interaction with the flavanols or because of their interaction with the salivary proteins.

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).

Influence of inactive dry yeast treatments during grape ripening on postharvest berry skin texture parameters and phenolic compounds extractability

Inactive dry yeast treatments in the vineyard are a tool used with the aim to improve the concentration and quality of secondary metabolites in grapes, leading to a better differentiation of the wines made from grapes differently treated. In this work, a foliar spraying treatment with yeast derivatives specifically designed to be used with the patent pending application technology of Lallemand Inc. Canada (LalVigne® Mature, Lallemand Inc., Montreal, Canada) was tested on Vitis vinifera L. cv. Barbera and Nebbiolo black winegrapes. The aim was to evaluate the effect of this treatment on the phenolic compounds accumulation, the skin physical-mechanical properties and the related phenolic extractability. Prior to analysis, the berries were sorted by flotation in order to evaluate their distribution by density class, and to determine the skin texture parameters of berries with different sugar contents, thus understanding also the ripening effect.