Gut Health & Fermented Foods – An Emerging Factor for Health and Disease Prevention?

By Published On: December 20, 2023
Gut Health & Fermented Foods – An Emerging Factor for Health and Disease Prevention?

The human microbiome, a community of more than 50 trillion bacteria and many more living microorganisms settled in and on our bodies, represents a pandora box of great mysteries. While a clear definition of a “healthy microbiome” does not yet exist, diversity has emerged as one major factor that enables the microbiome to support the immune system, provide nutrients and in some cases prevent certain diseases. Overall, these microorganisms play an important role in our lives and in the way our bodies function.

Specifically, dietary changes that improve the diversity of the gut microbiome can play an important role in preventing non-communicable diseases (NCDs). This article provides an overview on the gut microbiome’s impact on health and looks at how eating fermented foods can help promote positive impacts, bridging the connection between two ongoing EU-funded research projects studying how certain microbiomes can improve health in Europe.

Understanding the human microbiome’s impact on health

Over recent decades, chronic diseases have been on the rise across the world, presenting a major threat to public health. In particular, the health and longevity of the European population is facing increasing challenges due to the rising occurrence of non-communicable metabolic and degenerative diseases. This concerning rise of NCDs is attributed to a combination of factors, and according to the World Health Organization (WHO), the major NCDs (cardiovascular diseases, cancers, chronic respiratory diseases and diabetes) share four common modifiable risk factors: an unhealthy diet, physical inactivity, tobacco use and alcohol consumption1.

Preliminary research is exploring the connections between the human gut microbiome and the risk of developing NCDs. Considering the involvement of the microbiome in key metabolic and immunological processes, it could have a key role in preventing the onset of NCDs2. Nonetheless, notable gaps exist between progress in microbiome science and applications for healthcare professionals. This is further exacerbated by several challenges such as the lack of standardisation, the absence of a clear consensus on the concept of what defines a healthy microbiome (both in terms of how it functions and variety in microorganisms) in addition to a lack of common frameworks to develop biomarkers for providing proof of causality.3 Consequently, the impact of the human microbiome in regulating our health has not yet been fully uncovered.

The gut microbiome: what are its functions?

The gut microbiome, one of many human microbiomes, is gaining increased recognition for its pivotal role in influencing overall human well-being. It is crucial to nutrient absorption and immune function4. Researchers continue to document how the gut microbiome influences other organ systems, for example, the nervous system5. This has opened new avenues for addressing health concerns through targeted food and nutrition-based interventions and lifestyle choices. By focusing on the relationship between the gut microbiome and human health, we can expand the existing toolkits of knowledge and practices to combat NCDs and contribute to enhanced human well-being.

The gut microbiome contributes significantly to human well-being by the production of certain vitamins6 playing an important role in immune system development; assisting in the digestion of fibre-rich foods by breaking down complex sugars into simple nutrients7; creating a barrier effect in the intestine preventing the proliferation of environmental microorganisms and ensuring proper digestive functioning8.

Figure 1: Credit – The European Food Information Council (EUFIC)

Fermented foods: How do they impact our gut microbiome?

Fermented foods are emerging as one of the major foods choices that can modulate the gut microbiome, standing among other key influences such as hydration and fibre intake. Fermented foods are the resulting product of an intended and controlled fermentation of a raw material, aimed to extend a product’s shelf life and enhance new flavours while transforming it into a new product (cabbage into kimchi or sauerkraut, for example).

In the last few years, increasing amount of data evidenced the positive impact of fermented foods and their associated microbial communities on human health9. These studies highlight both the role of dietary microbiomes and their impact on the types of molecules resulting from the fermentation process. To improve relevant dietary recommendations based on fermented foods, further research is needed to understand the role of the food microbial diversity as an essential component for maintaining human health10.

Aside from live microbes, fermented foods offer other interesting bioactive compounds, for example, prebiotics. Prebiotics are resistant types of starches and complex sugars that our bodies cannot digest, but which the microorganisms living in our gut can benefit from, since these compounds act as their meal. Many fermented foods also contain bioactive peptides, which have promising outcomes on health such as reducing oxidative stress with their antioxidant effect11. For example, table olives are rich in polyphenols with significant antioxidant activity that can promote human health12.

Research in the field: a focus on two European-funded projects

To fully gain advantage from the potential benefits of the microbiome and fermented foods for human health, more research is essential. Two EU-funded projects, Human Microbiome Action and DOMINO, are at the forefront of this undertaking. Both projects the interplay between diet and microbiome as a lever for maintaining health and well-being and particularly its relevance in preventing and treating NCDs.

The Human Microbiome Action project aims to boost research and knowledge transfer in this field to combat the epidemics of chronic diseases. By harmonising how research is being conducted and by facilitating the bridging of information between key actors, the project enables binding conclusions regarding the microbiome and its role in the preservation of health. Another major outcome of the project is the settlement of a European Microbiome Centres Consortium that will act as a sharing hub for the harmonisation of processes and further discussions of the microbiome´s applications for the prevention of NCDs.

The DOMINO project intends to demonstrate the health impacts of fermented food-based diets on a healthy population to establish how fermented food consumption shapes the gut microbiome and provides health benefits to consumers. This project will contribute to a better understanding of how dietary recommendations based on fermented foods can support individuals with metabolic syndrome. DOMINO will also aim to better understand the metabolic interactions within fermented foods and their alignment with a healthy gut microbiome.


  1. World Health Organization: Noncommunicable diseases.
  2. Metwaly, A., Reitmeier, S., & Haller, D. (2022). Microbiome risk profiles as biomarkers for inflammatory and metabolic disorders. Nature Reviews Gastroenterology & Hepatology, 19(6), 383–397.
  3. Tap, J., Lejzerowicz, F., Cotillard, A., et al. (2023). Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors. Nature Communications, 14, 3310.
  4. Ding, R. X., et al. (2019). Revisit gut microbiota and its impact on human health and disease. Journal of Food and Drug Analysis, 27(3), 623–631.
  5. Farzi, A., Fröhlich, E. E., & Holzer, P. (2018). Gut microbiota and the neuroendocrine system. Neurotherapeutics: The Journal of the American Society for Experimental NeuroTherapeutics, 15(1), 5–22.
  6. Pham, V., et al. (2021). Vitamins, the gut microbiome and gastrointestinal health in humans. Nutrition Research, 95, 35–53.
  7. Fusco, W., et al. (2023). Short-chain fatty-acid-producing bacteria: Key components of the human gut microbiota. Nutrients, 15, 2211.
  8. Ghosh, S., et al. (2021). Regulation of intestinal barrier function by microbial metabolites. Cellular and Molecular Gastroenterology and Hepatology, 11(5), 1463–1482.
  9. Marco, et al. (2021). The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nature Reviews Gastroenterology & Hepatology, 18, 196–208.
  10. O’Donnell, et al. (2018). The use of a mini-bioreactor fermentation system as a reproducible, high-throughput ex vivo batch model of the distal colon. Frontiers in Microbiology, 9.
  11. Akbarian, M., et al. (2022). Bioactive peptides: Synthesis, sources, applications, and proposed mechanisms of action. International Journal of Molecular Sciences, 23(3), 1445.
  12. Rocha, et al. (2020). Table olives and health: A review. Journal of Nutritional Science, 9, e57.

This article was co-written by Domino and HMA researchers and published in both websites. 

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Advancing Microbiome Research: Highlights from the Workshop on Establishing Consensus for Microbiome Analysis Standards