Diet can affect your health and quality of life through acting on the gut microbiota

Thoughtful proverbs have always pointed out the connection between diet and health, but only more recently have we begun to uncover the mechanisms at work. The diet or food that we eat to nourish ourselves also sustains the growth and metabolism of our gut microbiota, which can affect our health.

Simply put, a diet is a description of the foods we eat. We hear about many trendy diets with suggested health benefits, including weight loss, improved immune and metabolic function, or gastrointestinal symptom improvement, such as the Mediterranean diet, ketogenic diets, low FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diet, and the gluten-free diet. There are also recommendations of caloric restriction or intermittent fasting (only eating in a small window of time) for improved energy, metabolic function, and weight loss.

However, restrictive diets are not without adverse effects, as they can lead to nutritional complications if not monitored by a health care expert. For instance, the gluten-free diet is medically indicated for patients diagnosed with celiac disease, but it requires expert dietician and physician assessment to mitigate the long-term nutritional deficiencies in fibre, vitamin D or iron that can contribute to complications (1). Likewise, it was recently shown that caloric restriction can increase the vulnerability to infections and increase bacteria that metabolize the protective mucus layer in the colon (2).

The messages in the media may be confusing to patients and the public, thus more research is needed to develop clear recommendations. This year, many exciting papers have been published regarding this topic.

In this summary we will focus on an emerging approach, rather than removing food components, supplementing our diet with fermented foods and prebiotic fibres that can support gut microbiota diversity.


Fermented foods for feeding a healthy gut microbiota

When we hear fermented foods, we may immediately think of foods like kombucha and probiotic yoghurt, but the truth is that breads, cheeses, meat, and even alcohol are fermented foods. It has been estimated that there are over 5000 varieties of fermented foods products globally (3)!

But what does fermentation mean, and why is it a key part of the food industry? In the context of making food, fermentation has a general definition that covers any sort of process using desired microbial growth and enzymatic conversions of food components. Historically the sometimes-accidental use of fermentation helped to create safer foods with longer shelf lives in regions of the world without clean water or electricity (4).

Today the selection of desirable microorganisms such as bacteria and yeasts to take advantage of the products derived from their metabolism (“starter cultures”) is a vital part in making unique yoghurts, sourdough breads, and kombucha brews with suggested health benefits through the gut microbiota. However, many fermented foods don’t contain any live microorganisms and they are not required to have a health benefit. Interestingly, the fermented foods that do influence the immune system tend to be further broken down by microbes into substances found in small amounts such as polyphenols with actions in the body that can promote good health (4).


So why are fermented foods gaining so much attention?

There is little clinical evidence in humans that specific fermented foods like kombucha or kimchi can consistently modify the microbiome to treat gastrointestinal diseases, partly due to the variation of microorganism cultures in different locations (5). However, there is some evidence that fermented foods can be beneficial when included as part of a diverse diet, for instance through their anti-inflammatory properties (6). While these results are not specific to any disease or genetic status, they may imply potential benefits in those with chronic inflammatory conditions.

The results from a recently published small longitudinal study in healthy adults showed that six servings a day of a variety of fermented foods increased gut microbiota diversity and reduced inflammation (7), although the study was limited by size and lack of suitable controls. Right now, there simply is not sufficient evidence to make clear recommendations to consume fermented foods for improving specific conditions, and caution should be applied, since an overload of such fermented foods could also trigger symptoms in some individuals.


What diet therefore is best for your gut microbiota?

The scientist’s favourite answer – “It depends!The gut microbiota is a complex fingerprint of the individual, both in composition and function, so there isn’t a single type of diet that will optimally support bacterial growth and metabolism for everyone.

To make educated decisions to feed ourselves, we must educate ourselves on our bacteria. The different communities harbored by an individual can ferment the same types of fibres at different rates, to produce distinct metabolites profiles that can affect the immune system (8). For example, we know that most patients with celiac disease on a long-term gluten-free diet may require nutritional support, but supplementation with the wrong type of fibre could lead to bloating or constipation.

Is this because of the bacteria, or the type of fibre? It may be one or the other, or even both. In the future, when practice catches up with theory, we may be able to use individualized diets tailored to our specific gut bacteria. We need to learn more about how microbial profiles associated with health can be influenced by diet or disease. A large study (Personalized Responses to Dietary Composition Trial (PREDICT-1)) used fecal metagenomic sequencing to investigate the effects of long-term diet patterns and found many strong microbial associations with specific foods in the UK that were validated in the US (9). Still, more studies are needed on how specific food components, such as fermented foods or fibres, are utilized by the gut microbiota so that we can make effective recommendations for patients.


Take-Home Messages:

  • A diverse, balanced diet is a sensible approach to support gut and microbiome health as long-term restrictive diets may cause nutritional deficiencies.
  • Fermented food products historically increased the shelf-life and safety of foods.
  • Fermented foods can increase gut microbial diversity and reduce host immune responses, but in some individuals they may trigger gastrointestinal symptoms.
  • Understanding diet-microbiome interactions and how they work will help us advance towards precise diet-microbiome modulation for optimal health.



1.Cardo A, Churruca I, Lasa A, Navarro V, Vázquez-Polo M, Perez-Junkera G, et al. Nutritional imbalances in adult celiac patients following a gluten-free diet. Nutrients. 2021; 13(8):2877. doi: 10.3390/nu13082877.

2.von Schwartzenberg RJ, Bisanz JE, Lyalina S, Spanogiannopoulos P, Ang QY, Cai J, et al. Caloric restriction disrupts the microbiota and colonization resistance. Nature. 2021; 595(7866):272-277. doi: 10.1038/s41586-021-03663-4.

3.Tamang JP, Watanabe K, Holzapfel WH. Review: Diversity of microorganisms in global fermented foods and beverages. Front Microbiol. 2016; 7:377. doi: 10.3389/fmicb.2016.00377.

4.Marco ML, Sanders ME, Gänzle M, Arrieta MC, Cotter PD, De Vuyst L, et al. The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods. Nat Rev Gastroenterol Hepatol. 2021; 18(3):196-208. doi: 10.1038/s41575-020-00390-5.

5.Dimidi E, Cox SR, Rossi M, Whelan K. Fermented foods: Definitions and characteristics, impact on the gut microbiota and effects on gastrointestinal health and disease. Nutrients. 2019; 11(8):1806. doi: 10.3390/nu11081806.

6.SaeidiFard N, Djafarian K, Shab-Bidar S. Fermented foods and inflammation: A systematic review and meta-analysis of randomized controlled trials. Clin Nutr ESPEN. 2020; 35:30-39. doi: 10.1016/j.clnesp.2019.10.010.

7.Wastyk HC, Fragiadakis GK, Perelman D, Dahan D, Merrill BD, Yu FB, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021; 184(16):4137-4153.e14. doi: 10.1016/j.cell.2021.06.019.

8.Chen T, Long W, Zhang C, Liu S, Zhao L, Hamaker BR. Fiber-utilizing capacity varies in Prevotella– versus Bacteroides-dominated gut microbiota. Sci Rep. 2017; 7(1):2594. doi: 10.1038/s41598-017-02995-4.

9.Asnicar F, Berry SE, Valdes AM, Nguyen LH, Piccinno G, Drew DA, et al. Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals. Nat Med. 2021; 27(2):321-332. doi: 10.1038/s41591-020-01183-8.