What is a ‘microbiome’, and how does it relate to wine?

Karien O’Kennedy

Have you ever wondered what gives your favorite bottle of wine its distinct character? Part of the answer lies in a world invisible to the naked eye but crucially helping to shape the taste and quality of wines: the microbiome.

But hold on, what exactly is a microbiome?

The terms ‘microbiome’ and ‘microbiota’ are often used interchangeably, but they actually refer to different aspects of microbial communities within a particular environment, such as the human body or vineyard soil. Microbiota refers to the collection of microorganisms, including bacteria, fungi, yeasts and viruses inhabiting a specific ecological niche. It focuses on the organisms themselves rather than their genetic material.

On the other hand, microbiome refers to the collective genetic material of all microorganisms present in a particular environment. It encompasses not only the microorganisms themselves but also their genes and their interactions with each other in their host environment. The microbiome provides a more holistic view of microbial communities, incorporating their genetic diversity and ecological functions. 

Microbiomics, the newest kid on the microbiology block, is the science of collectively characterising and quantifying molecules responsible for a microbial community’s structure, function, and dynamics.1 Microbiomics employs multiple techniques, including high-throughput sequencing, bioinformatics, and systems biology approaches, to investigate microbial communities and their interactions with their hosts and environments. The field has broad applications in human health, agriculture, environmental science, biotechnology, and beyond, with implications for understanding disease mechanisms and ecosystem dynamics and developing novel therapies and interventions.


Now, how does this relate to wine?

The vineyard microbiome plays a crucial role in shaping the unique characteristics of wines.2 The microbiome of the vineyard soil, grapevine, and grapes influences the health and growth of the grapevine and the composition of the grapes. The grape microbiome determines the fermentation microbiome (if no commercial yeast inoculation occurs) and the character of what finally ends up in your glass. 


Vineyard soils, the foundation of wine character

Soils harbour some of the most diverse microbiomes on earth. Observations from studies suggest that different vineyard soil microbiomes can contribute to variations in grape and wine composition and the wine’s terroir. This happens through the vines’ response to the soil microbiome or through the soil microbiome affecting the grape microbiome and, thus, fermentation.3 An example is an Australian study that demonstrated that distinct differences in the bacterial and fungal communities in different zones within the same vineyard are associated with high and low rotundone concentrations in grape berries. Rotundone is an impact aroma compound with a ‘peppery character’ commonly found in cool climate Shiraz from Australia. 

Various abiotic factors, such as geographical origin, climatic conditions, soil composition, and cultivation, can influence the vineyard soil microbiome. Interestingly, biotic factors can also play a significant role, with certain soil fungi that can impose a strong selection on bacteria by producing antimicrobial (antibiotic) compounds.4

Soil health is of utmost importance, not only for viticulture but for all agricultural systems. The soil microbiome forms a critical component of soil health. Understanding how agricultural systems, including viticulture, impact the soil microbiome is crucial to ensuring more sustainable agriculture and food for future generations. 


Grapevines, the guardians of wine character

Various factors can influence the microbiome of vines. Vineyard location, farming systems (conventional, organic, biodynamic), viticultural practices and even grape variety are among these factors. A study on Cabernet Sauvignon grapes in four countries with different climates and viticultural traditions using the same experimental layout suggested that grape varieties can have unique microbial fingerprints.2

The different parts of the vine can host various pathogenic and beneficial microorganisms. Beneficial microorganisms can help promote vine health by suppressing the growth of pathogenic organisms and enhancing the plant’s resistance to diseases.5 Studying these interactions can pave the way for eco-friendly biological control of grapevine diseases instead of chemical control. Studying the microbiome in vineyards also holds the potential to improve grapevine adaptation to climate change and boost overall sustainability. 


Fermentation, where the magic happens

Microorganisms present on grape surfaces can contribute to the initial stages of fermentation by inoculating grape must with indigenous yeast and bacteria. These native microorganisms initiate spontaneous fermentation, which can influence the chemical composition of the wine, such as its acidity, alcohol content and phenolic profile. Additionally, the microbial communities present during fermentation can lead to the development of complex flavours, aromas and textures in the resulting wine. 

Any given species’ contribution to the wine’s final character depends on its numbers and persistence during fermentation. Many factors can influence these two aspects, including interspecies ecological interactions, as shown by South African and Italian researchers.6 Studying the grape juice and fermentation microbiome and the factors that influence it can give winemakers the tools to steer the fermentation in a positive direction for wine quality. It can also help prevent fermentation problems such as stuck fermentations and the formation of off-odours.


Biodiversity for a sustainable future

In the coming decades, the agricultural sector will face major challenges in providing food for a growing world population, but intensive cropping, based on mineral fertilisers and agrochemicals, will continue to impact biodiversity and ecosystems negatively.7 Wine production is no exception to these environmental problems. The study of microorganisms in vineyards and wine production reveals the essential contribution of these invisible communities to the functioning and sustainability of viticultural systems. Microorganisms are vital players in achieving optimal outcomes with diverse influences, from soil health and vine vitality to fermentation and the sensorial profile of a wine. Their complex and symbiotic interaction with the viticultural environment triggers a range of benefits, including the enhancement of final product quality and vineyard resilience against adverse factors.  Understanding the factors that impact microbiome distribution and microbial diversity is essential to better harness natural ecosystems for quality wine production.


[1] Kumar PS. Microbiomics: Were we all wrong before? Periodontol 2000. 2021;85(1). doi:10.1111/prd.12373

[2] Tronchoni J, Setati ME, Fracassetti D, Valdetara F, Maghradze D, Foschino R, et al. Identifying the Main Drivers in Microbial Diversity for Cabernet Sauvignon Cultivars from Europe to South Africa: Evidence for a Cultivar-Specific Microbial Fingerprint. Journal of Fungi. 2022;8(10). doi:10.3390/jof8101034

[3] Gupta VVSR, Bramley RGV, Greenfield P, Yu J, Herderich MJ. Vineyard soil microbiome composition related to rotundone concentration in Australian cool climate “peppery” Shiraz grapes. Front Microbiol. 2019;10(JULY). doi:10.3389/fmicb.2019.01607

[4] Bahram M, Hildebrand F, Forslund SK, Anderson JL, Soudzilovskaia NA, Bodegom PM, et al. Structure and function of the global topsoil microbiome. Nature. 2018;560(7717). doi:10.1038/s41586-018-0386-6

[5] Cobos R, Ibañez A, Diez-Galán A, Calvo-Peña C, Ghoreshizadeh S, Coque JJR. The Grapevine Microbiome to the Rescue: Implications for the Biocontrol of Trunk Diseases. Plants. 2022;11(7). doi:10.3390/plants11070840

[6] Bagheri B, Bauer FF, Cardinali G, Setati ME. Ecological interactions are a primary driver of population dynamics in wine yeast microbiota during fermentation. Sci Rep. 2020;10(1). doi:10.1038/s41598-020-61690-z

[7] García-Izquierdo I, Colino-Rabanal VJ, Tamame M, Rodríguez-López F. Microbiota Ecosystem Services in Vineyards and Wine: A Review. Agronomy 2024, Vol 14, Page 131. 2024;14(1):131. doi:10.3390/AGRONOMY14010131

About the author:

Dr Karien O’Kennedy is the Knowledge Transfer Manager for South Africa Wine, an Associated Partner of the Eco2Wine project (https://cordis.europa.eu/project/id/101119480). She holds an MSc in Microbiology and a PhD in Science and Technology Studies from Stellenbosch University, South Africa. Her areas of expertise include wine microbiology and academic knowledge production, transfer, and uptake.