NATURE Scientific Reports | Robin Mesnage, Jérôme Douzelet, Gilles-Eric Seralini | February 10, 2025
Abstract
Fermentation produces diverse consumables like bread, wine, beer, and cheese, with fungi playing a key role. This study sequenced fungal and bacteria DNA from 46 commercial wines, paired by vineyard proximity, harvest time, and grape variety. One in each pair was natural, while the other had pesticide treatments and microbial adjunctions. Bacteria profiles were studied using targeted sequencing of the V3-V4 region of the 16 S rRNA gene while fungal profiles were studied with ITS gene targeted sequencing. Significant variability was observed in the microbial content of these wines. We identified 19 unique fungal species in natural wines, absent in pesticide-treated ones. Some have known health roles. The most abundant was Penicillium jiangxiense in Lot-et-Garonne, known for its antitumor properties. Hyphopichia pseudoburtonii, with notable aromatic properties, was also detected, commonly found in insect and fish microbiota. Antrodia favescens, related to the medicinal Antrodia cinnamomea, was identified in another location, known for its role in Chinese herbal medicine against cancer and metabolic diseases. Ochrocladosporium elatum, recognized for its antioxidant and antibacterial activities, was found elsewhere. Additionally, natural wines exhibited greater bacterial biodiversity, contributing to unique tastes and potential health benefits.
Introduction
Microbial communities, particularly fungi, play a crucial role in the fermentation-digestion processes of various foods and beverages. These communities initiate the transformation of plant-based substrates into natural products, generating a wide array of consumables such as bread, wine, beer, cheese, coffee, vanilla, and kefir. Beyond kickstarting fermentation, fungi significantly enhance the sensory qualities and shelf life of these products. Small quantities of alcohol produced during fermentation can inhibit the growth of certain pathogens, while fermentation within the gut microbiota contributes to digestion and the production of essential micronutrients. Current research underscores the vital symbiotic relationship between the gut microbiota and its host, impacting neurological functions, immunity, vitamin synthesis, and detoxification processes1.
The microbial communities associated with grapes and wine have been extensively studied, given their indispensable role in fermentation, a practice dating back at least 7,000 years2. Recent technological advancements have improved the selection and modification of microorganisms for commercial use, including CRISPR gene editing techniques3. In contrast, natural fermentations increasingly utilize atypical grape varieties worldwide, including regions like Chile4, India5, and Europe (Italy, Greece, Austria, France).
Natural fermentations, characterized by the absence of commercial fungi, bacteria, artificial compounds, or pesticides, promote a unique microbial biodiversity. This practice not only defines natural wines but also supports sustainable viticulture by enhancing ecological services and reducing dependence on external inputs6. Despite the recognized properties of these microbial communities, many potential benefits, including their roles against pathogenic agents, remain largely unexplored7.
Wine bottles harbor a complex array of microorganisms originating from fermentation and winemaking practices. During fermentation, indigenous yeasts, predominantly Saccharomyces cerevisiae and non-Saccharomyces species such as Hanseniaspora and Candida, drive the conversion of sugars into ethanol, alongside bacteria like Oenococcus oeni8. Emerging evidence suggests natural fermentation supports a richer microbial ecosystem, including Enterobacteriaceae, Pseudomonas, Sphingomonas, and Methylobacterium which could contribute to wine characteristics directly or indirectly9. In contrast, conventional winemaking often relies on inoculated commercial starters that either include Saccharomyces or lactic acid bacteria (e.g. Oenococcus oeni) and controlled microbial activity to standardize fermentation and ensure consistency10. Despite these differences, no comprehensive study has compared the microbial composition of naturally fermented wines to conventional wines derived from pesticide-treated grapes.
In this novel investigation, we performed a comparative analysis of the microbiota composition in natural wines and for the first time those neighbouring derived from grapes treated with pesticides. Uniquely, each sample pair originated from the same grape variety, same harvest year, and vineyard geolocation (acting as very close plots within a similar ecosystem). This approach is distinct from previous studies which focused solely on pesticide residues in the final product11 and their taste. This approach allows a more controlled exploration of how pesticides influence the raisin and wine microbiota. In other previous comparable studies, we have already studied the pesticide content in the bottles of closely neighbouring wineyards treated or not, and also characterized the presence, taste and effects not only of many pesticides, but also of sulfur residues and copper12,13.
In light of the growing interest in the influence of agricultural practices, taking into account not only climate change, but also gut microbiota, this research presents a unique opportunity to investigate the intrinsic microbial communities of naturally all grown fruits and vegetables, compared to commercially available pesticide-treated products.
Originally published in Nature, please click here to read more.
Mesnage, R., Douzelet, J. & Seralini, GE. Comparative analysis of fungal and bacterial composition in natural wines and their closest pesticide-treated counterparts. Sci Rep15, 4877 (2025). https://doi.org/10.1038/s41598-025-88655-4