BLOG BY Charlotte Green, BSc

An Introduction to the Gut Microbiota

In recent years, evidence has demonstrated the important role of the gut in maintaining good general health. It is thought that this is largely due to the influence of the gut microbiota, the community of trillions of microorganisms that reside along the digestive tract. In fact, our bodies contain ten times more microbes than human cells, with the majority of species working symbiotically with us to maintain our health.1 Although bacteria are the most widely studied and spoken about, the gut microbiota is also composed of many species of fungi, viruses and protozoans.2 Colonisation of the gut begins at birth and is subsequently influenced by many lifestyle factors including diet and our environment, meaning each person’s gut microbiota is unique.3

What can the gut microbiota do for us?

One of the most important roles of the gut microbiota is in digestion. There are certain types of fibre found in plant-based foods, such as lignin, resistant starch and fructooligosaccharides that our own bodies cannot digest, but our gut microbes can.1 Some dietary fibres, known as prebiotics, found in foods like bananas, leeks, garlic, onions and oats, act as fuel for the microbes themselves. This allows the beneficial species to thrive, whilst allowing us to obtain the maximum amount of energy and nutrients from the food we eat.4

Furthermore, the digestion of these fibres produces beneficial compounds known as short chain fatty acids (SCFAs). SCFAs can leave the digestive system and enter the circulation, meaning the gut microbiota can have wider influences in other areas of the body.

For instance, SCFAs:

• signal via the central nervous system to affect carbohydrate and fat metabolism

• have anti-inflammatory properties3

• regulate appetite by activating the release of leptin, the hormone which signals fullness5

• control the release of serotonin in the gut, therefore affecting mood and sleep1

Additionally, another family of plant compounds known as polyphenols, abundant in berries, tea, coffee, cocoa and red wine, are also broken down by the gut microbiota.2 This process activates the polyphenols, enabling them to act as anti-oxidants, reducing damage to cells. They have also been shown to be effective at protecting against cardiovascular disease, due to their anti-inflammatory properties.6 Consequently, a healthy gut microbiota is integral to obtain the health benefits from the consumption of polyphenols.

Aside from digestion, the gut microbiota plays an important role in the function of the immune system. This is because the resident beneficial species can communicate with each other via specialised molecules to maintain their own communities whilst preventing the colonisation of harmful microbes and subsequent infections.7

The Gut-Brain Axis

There is a complex, two-way communication system between the gut and the brain, which the gut microbiota is heavily involved in. For example, the microbiota is able to modulate the gut to brain signalling network via metabolites such as SCFAs. However, in the other direction, signals transmitted along the parasympathetic nervous system, part of the autonomic nervous system which controls automatic functions in the body, can modulate the composition of the gut microbiota by altering the intestinal environment.8 Consequently, it has been postulated that changes in the gut microbiota could be associated with the development of mood disorders such as depression and neurodegenerative conditions like Alzheimer’s Disease.8 Although there is some evidence to support this, most experiments so far have only been carried out using animal models. This means that a significant amount of further research is required to confirm the specific link between the gut microbiota and brain health before the development of treatments that target the gut microbiota for conditions like depression.9

How can we support our gut microbiota?

The composition of the gut microbiota and the abundance of beneficial species is largely influenced by lifestyle factors, especially diet. This means that simple changes can nourish our resident microorganisms, therefore benefitting our gut and general health.

•One of the best ways to take care of the gut microbiota is by making the diet as varied as possible, with a particular focus on plant-based foods. This is because different bacterial species use different plant-based fibre for energy and growth, so a diverse diet means a diverse microbiota.3 This can be achieved by including a range of different fruits, vegetables, wholegrains, nuts, seeds, and legumes. It is recommended that 30 different plant foods should be included in the diet every week.

• Try to include sources of polyphenols, which have not only been shown to increase the abundance of beneficial Bifidobacterium and Lactobacillus species, but also have wider anti-inflammatory properties in the body.6 Foods rich in polyphenols include berries, apples, coffee, tea, red wine and extra virgin olive oil.

• Be conscious of the consumption of large amounts of ultra-processed foods. These foods are generally higher in saturated fat and sugar, but when considering the gut microbiota, attention should also be paid to food additives often used in these products. There is some evidence to suggest that they can negatively affect the composition and metabolism of the gut microbiota, therefore reducing diversity.3

• In recent years, fermented foods such as kimchi, kombucha (fermented tea) and kefir have gained popularity, due to being marketed as good for gut health. However, at the moment, there is limited evidence to suggest that they can have a significant impact on the gut microbiota, apart from fermented dairy products.10 Nevertheless, if you enjoy the taste of fermented foods, they are still a nutritious and delicious addition to the diet.

• Again, another industry that has boomed as a result of a growing interest in gut health is probiotic supplements. These are live microorganisms, usually taken in capsule or liquid form, and are being increasingly taken by individuals who do not have any particular health concerns. However, there is very limited clinical evidence that they have a beneficial health impact outside of a few selected medical conditions. For instance, there is some evidence for the use of probiotics to relieve symptoms of IBS, as this condition can sometimes develop due to an imbalance of different species in the microbiota. However, it is still unclear which bacterial strains are the most effective.11 Consequently, in people who are generally healthy, it is much better to focus on a varied balanced diet to nourish the microbiota.

• Finally, the involvement of the gut microbiota in the gut-brain axis, means that other lifestyle factors like sleep quality and stress management should be addressed to optimise the microbiota.

This article was written by Charlotte Green, a final year undergraduate studying Biological Sciences at Durham University. She is particularly interested in the role of the gut microbiota in health and how nutrition influences this, so hopes to pursue a Master's degree in nutrition once she graduates. Charlotte has developed a passion for science communication and is also a guest contributor to the @forkingwellness Instagram page. You can find her on Instagram @charlottevictoria23.


1.        Adak, A. & Khan, M. R. An insight into gut microbiota and its functionalities. Cellular and Molecular Life Sciences vol. 76 473–493 (2019).

2.        Jandhyala, S. M. et al. Role of the normal gut microbiota. World J. Gastroenterol. 21, 8836–8847 (2015).

3.        Gentile, C. L. & Weir, T. L. The gut microbiota at the intersection of diet and human health. Science vol. 362 776–780 (2018).

4.        Davani-Davari, D. et al. Prebiotics: Definition, types, sources, mechanisms, and clinical applications. Foods vol. 8 (2019).

5.        Brownawell, A. M. et al. Prebiotics and the health benefits of fiber: Current regulatory status, future research, and goals. J. Nutr. 142, 962–974 (2012).

6.        Sakkas, H. et al. Nutritional status and the influence of the vegan diet on the gut microbiota and human health. Medicina (Lithuania) vol. 56 (2020).

7.        Wu, L. & Luo, Y. Bacterial Quorum-Sensing Systems and Their Role in Intestinal Bacteria-Host Crosstalk. Front. Microbiol. 12, 611413 (2021).

8.        Osadchiy, V., Martin, C. R. & Mayer, E. A. The Gut–Brain Axis and the Microbiome: Mechanisms and Clinical Implications. Clinical Gastroenterology and Hepatology vol. 17 322–332 (2019).

9.        Mayer, E. A., Tillisch, K. & Gupta, A. Gut/brain axis and the microbiota. Journal of Clinical Investigation vol. 125 926–938 (2015).

10.      Fermented Foods - The Gut Health Doctor. https://www.theguthealthdoctor.com/fermented-foods/.

11.      Mizock, B. A. Probiotics. Disease-a-Month vol. 61 259–290 (2015).

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