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…

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.

Ellagitannins and flavano-ellagitannins: concentration ranges in different areas and sensory evaluation

C-Glucosidic ellagitannins, which are the main polyphenolic compounds in oak heartwood, are extracted by wine during aging in oak barrels. Although such maturing of alcoholic beverages in oak barrels is a multi-centennial practice, very little is known on the impact of these ellagitannins on the organoleptic properties of red wine. The objectives of the present investigation were (i) to isolate oak ellagitannins and to hemisynthesize some made-in-wine flavano-ellagitannins, such as acutissimin A; (ii) to analyse their concentration ranges depending on the cultivar area and (iii) to evaluate their sensory impact on the basis of their human threshold concentrations and dose/response relationships in different types of solutions.

Multivariate strategies for red wines classification using stilbenes and flavonols content

Bioactive polyphenols from grapes and wines, like stilbenes and flavonols (SaF), are often determined to nutritional evaluation, but also for many other purposes. The objective of this study was to quantify SaF in red wines from “Campanha Gaúcha”, a large and young viticultural region from South Brazil. Moreover, through statistical analysis, evaluate the influence of these compounds according to varieties, production process, harvest years and micro-regions of cultivation. A total of 58 samples of red wines were analyzed by high-performance liquid chromatography coupled to diode array detector (HPLC-DAD) for determination of trans-resveratrol (R), quercetin (Q), myricetin (M), kaempferol (K), trans-e-viniferin (V) and their precursor, cinnamic acid (C).

Oligosaccharides in red wines: could their structure and composition be influenced by the grape-growing

Oligosaccharides have only recently been characterized in wine, and the information on composition and content is still limited. In wine, these molecules are mainly natural byproducts of the degradation of grape berry cell wall polysaccharides. Wine oligosaccharides present several physicochemical properties, being one relevant factor linked to the astringency perception of wines (1,2). A terroir can be defined as a grouping of homogeneous environmental units based on the typicality of the products obtained. This notion is particularly associated with wine, being the climate and the soil two of the major elements of terroir concept.

Removal of Fumonisin B1 and B2 from red wine using polymeric substances

The Ability of PVPP (Polyvinylpolypyrrolidone), PVP-DEGMA-TAIC (copolimerization of N-vinyl-2-pyrrolidinone with ethylene glycol dimethacrylate and triallyl isocyanurate) and PAEGDMA
(poly(acrylamide-co-ethylene glycol dimethacrylate)) polymers was tested as removal agents for Fumonisin B1 (FB1) and Fumonisin B2 (FB2) from model solutions and red wine. The polymers removal capacity was checked at three different resident times (2, 8 and 24 hours of contact time between the polymer and the sample), showing no differences in the percentage of FB1 and FB2 removal. Then, different polymer concentrations (1, 5 and 10 mg mL-1) were tested in model solution with and without phenolics (i.e. gallic acid and 4-methylcatechol).