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 varying ethanol and carbonation levels on the odor threshold of 1,1,6-trimethyl-1,2-dihydronaphtalene (petrol off-flavor) and role of berry size and Riesling clones

1,1,6-trimethyl-1,2-dihydronaphtelene (TDN) evokes the odor of “petrol” in wine, especially in the variety Riesling. Increasing UV-radiation due to climate change intensifies formation of carotenoids in the berry skins and an increase of TDN-precursors1. Exploring new viticultural and oenological strategies to limit TDN formation in the future requires precise knowledge of TDN thresholds in different matrices. Thresholds reported in the literature vary substantially between 2 µg/L up to 20 µg/L2,3,4 due to the use of different methods. As Riesling grapes are used for very different wine styles such as dry, sweet or sparkling wines, it is essential to study the impact of varying ethanol and carbonation levels.

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).

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.

DNA and type of grain: which factor does better explain sensory differences of sessile and pedunculate oaks?

Sessile oak and pedunculate oak have shown several differences of interest for enological purposes. Tannic and aromatic composition among sessile oak or pedonculate oak has been well studied. Sessile oak is generally more aromatic than pedunculated, while the later is more tannic. This scientific point of view is rarely applied to classify oak in cooperages. Most coopers use the type of grain to distinguish wide and thin grain.

Extraction of pathogenesis-related proteins and phenolics in Sauvignon Blanc as affected by different

The composition of wine is largely determined by the composition of pre-fermentation juice, which is influenced by extraction of grape components. Different grape harvesting and processing conditions could affect the extraction of grape components into juice. Among these grape components, pathogenesis-related (PR) proteins are of great concern for white wine maker as they are the main cause of haze formation in finished white wine. If not removed before bottling, these PR proteins may progress into haze through the formation of complex with phenolics under certain conditions. Thaumatin-like proteins (TLPs) and chitinases are the main constituents of PR proteins found in protein haze.