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The Gut Microbiome and How to Help it Thrive

Unless you have been living as a recluse, you can hardly have failed to notice the current interest in the gut microbiome, that collection of microbes (including bacteria, fungi, archaea and viruses) inhabiting our gastrointestinal tract, especially in our large intestine.  In this blog, I’m aiming to explain some of the links between the gut microbiome and cancer and help you to consider factors that may have been protective of or harmful to your own gut microbiome. Finally, and most importantly, there will be ideas for looking after this important ecosystem inside you!

What is a Healthy Gut Microbiome?

The gut microbiome is so complex that a healthy gut microbiome has not been clearly defined. However, we do know that people who are in good health tend to have microbiomes that contain a greater diversity of microbes than people with various medical conditions(1). Conditions as diverse as IBS, type 2 diabetes and cancer have all been associated with alterations in the gut microbiome.

Gut Microbiome Links to Cancer

There are some pathogens that can inhabit the human gut that are known to have a causative role in specific cancers. For example, fusobacterium nucleatum is implicated in colorectal cancer and salmonella typhi in hepatobiliary cancers(2). However, most of the links between the gut microbiome and cancer do not take the form of a direct cause and effect relationship between a single microbe and cancer.

The gut microbiome as a whole can affect multiple factors involved in the development and progression of cancer. For example, it affects the balance between cell proliferation and death; it is instrumental in controlling the immunity of the host (you!); and it controls your immunity(2).

In breast cancer, the gut microbiome influences circulating oestrogen levels because certain gut bacteria can prevent used oestrogens from being excreted from the body. Compounds in foods such as soy and flaxseeds require specific gut bacteria to convert them into phytoestrogens.

When it comes to the importance of the gut microbiome during cancer treatment, there is now considerable evidence that the gut microbiome influences how successful immunotherapy is(3). There is some evidence, although much less, that the gut microbiome also affects chemotherapy outcomes and side effects, although we do not yet have enough knowledge yet on how best to influence the gut microbiome for optimum chemotherapy outcomes(4). There has also been research showing that the composition of the gut microbiome influences long-term as well as short-term outcomes after colorectal cancer surgery(5), (6).

Not only does the gut microbiome affect cancer treatment, but treatment can have a profound effect on the gut microbiome. Chemotherapy directly changes the microbiome, and drugs frequently used alongside chemotherapy, such as antibiotics or anti-sickness medications, can also have an effect.

Factors which adversely affect the gut microbiome

Early life, often thought of as the first thousand days after conception, is key in establishing the gut microbiome. Protective factors during this window of opportunity include being born vaginally and being breastfed, having pets and older siblings, and not living in an overly clean environment (some exposure to common microbes is helpful in training the immune system in the gut)(7). Antibiotics, although often life-saving, can severely disrupt the gut microbiome at any time in life, but early life exposure may be particularly detrimental.

Later in life, a lack of physical activity, environmental pollution, stress and alcohol are among factors that can have adverse consequences for the microbiome. It should come as no surprise that diet has a profound and rapid effect on the gut microbiome(8). The microbiome is not completely static; variations can be measured depending on the previous meal eaten.

How to support your gut microbiome with diet - prebiotics

A diverse microbiome is associated with health, so our aim is to cultivate diversity. Different beneficial microbes like to ferment different fibres (which we humans cannot digest). Therefore, to encourage beneficial microbes to continue living in your gut, you have to provide them with their preferred fibres. Encouraging microbiome diversity therefore involves eating as wide a variety of fibres as possible, from vegetables, fruits, whole grains, nuts, seeds and legumes.

The American Gut Project looked at associations between diet and human gut microbiome samples. They found that the people with the most diverse gut microbiomes tended to eat at least 30 different plants each week(9). Again, plants can be vegetables, fruits, whole grains, nuts, seeds, legumes, herbs and spices. Why not log down each different plant you eat for a week and see how close you come to 30?

The fibres which feed beneficial gut microbes are called prebiotic fibres. Although all plant foods are helpful, foods which are particularly high in prebiotic fibres include:

  • Jerusalem artichokes

  • Asparagus

  • Leeks, onions and garlic

  • Pulses (chickpeas, beans and lentils)

  • Chicory

  • Green banana

  • Flaxseeds

As well as supporting gut microbiome diversity, prebiotics can also provide benefits for cognition, mood, immunity, cholesterol and skin health(10). As a more diverse gut microbiome is associated with better immunotherapy outcomes, eating a wide variety of plant fibres is very important before and during immunotherapy.

If you find foods that are high in prebiotic fibre difficult to tolerate, then start with very, very small quantities. If your gut can cope with this, then you can increase very gradually. There are also foods that feed beneficial gut microbes other than by their fibre content; these can also be thought of as prebiotics, and might be easier to tolerate for those with sensitive guts. They include oily fish (for their omega 3 fatty acid content), herbs, spices, tea (green and black) and cocoa.

How to support your gut microbiome with diet – fermented foods

An interesting study in 2021 compared the impact of a diet high in fibre to a diet high in fermented foods for 17 weeks. By the end of the study, increasing dietary fibre had led to signs that the microbiome was being remodelled, but an increase in diversity had not actually occurred. The study authors speculated that the timescale may not have been long enough, and that a longer high fibre intake may have led to increased diversity over time.

In contrast, the diet high in fermented foods resulted in increased microbiome diversity, as well as a decrease in inflammation, during the study period(11). This suggests that whilst, long term, it is important to eat a wide variety of plant fibres, incorporating fermented foods into your diet may be a quicker route to increasing the diversity of your microbiome.

Fermented foods can be fun to make yourself, but they are also increasingly easy to find in supermarkets as well as in health food shops. Options include:

  • Sauerkraut: fermented cabbage, and in my opinion the easiest fermented food to make at home

  • Kimchi: a spicy Korean fermented food usually containing cabbage, radish, chilli flakes and sometimes fish sauce

  • Live Yoghurt

  • Kefir: a fermented milk product in the form of a drink or as a more solid yoghurt-like consistency

  • Kombucha: fermented green tea, which is a great alternative to alcoholic drinks or sugary soft drinks

If you are buying fermented vegetables, make sure that they are really fermented and not pickled. Pickled vegetables will contain vinegar whereas fermented vegetables will not. Brands that I love include The London Fermentary (, The Cultured Collective (, Vadasz ( and Hurly Burly.

If you have never eaten fermented foods before, then start slowly! It is better to have small amounts of fermented foods regularly than to have a large portion all at once.

If you are currently having chemotherapy and are frequently neutropenic, please seek advice from a healthcare practitioner before eating fermented foods. If you are having immunotherapy, such as a checkpoint inhibitor, then please also seek advice from a nutrition professional.

And finally

Remember that there are also non-dietary approaches which can support your gut microbiome. Exercise, meditation, and spending time in nature (or even around more garden plants!) can all have positive effects. Avoiding smoking is important, as is looking after your dental hygiene (we swallow some of the microbes that are in our mouth so they affect the gut too).

Just like a garden, cultivating a diverse gut microbiome requires your attention. When you are shopping or planning your meals, how about considering not just what you are feeding yourself, but what you will be feeding your gut microbes? They provide you with so many health benefits, so look after them!

Gut microbiome after cancer


(1)    Hills Jr., R.D., Pontefract, B.A., Mishcon, H.R. et al. (2019). ‘Gut Microbiome: Profound Implications for Diet and Disease’, Nutrients, 11(7):1613. Available at (Accessed 27 February 2024).

(2)    Viswanathan, S., Parida, S., Lingipilli, B.T. et al. (2023). ‘Role of Gut Microbiota in Breast Cancer and Drug Resistance’, Pathogens, 12(3), 468. Available at (Accessed 25 February 2024).

(3)    Roviello, G., Iannone, L.F., Bersanelli, M. et al. (2022). ‘The gut microbiome and efficacy of cancer immunotherapy’, Pharmacology & Therapeutics, 231:107973. Available at (Accessed 26 February 2024).

(4)    Huang, J., Liu, W., Kang, W. et al. (2022). ‘Effects of microbiota on anticancer drugs: Current knowledge and potential applications’, eBioMedicine, 83:104197. Available at (Accessed 26 February 2024).

(5)    Lauka, L., Reitano, E., Carra, M.C. et al. (2019). ‘Role of the intestinal microbiome in colorectal cancer surgery outcomes’, World Journal of Surgical Oncology, 17(1):204. Available at (Accessed 26 February 2024).

(6)    Colov, E.P., Degett, T.H., Raskov, H. et al. (2020). ‘The impact of the gut microbiota on prognosis after surgery for colorectal cancer - a systematic review and meta-analysis’, APMIS, 128(2), pp162-176. Available at (Accessed 26 February 2024).

(7)    Tanaka, M. and Nakayama, J. (2017). ‘Development of the gut microbiota in infancy and its impact on health in later life’, Allergology International, 66(4), pp515-522. Available at (Accessed 26 February 2024).

(8)    Wilson, A.S., Koller, K.R., Ramaboli, M.C. et al. (2020). ‘Diet and the Human Gut Microbiome: An International Review’, Digestive Diseases and Sciences, 65(3), pp723-740. Availabl at (Accessed 27 February 2024).

(9)    McDonald, D., Hyde, E., Debelius, J.W. et al. (2018). ‘American Gut: an Open Platform for Citizen Science Microbiome Research’, mSystems, 3(3): e00031-18. Available at (Accessed 27 February 2024).

(10)Davani-Davari, D., Negahdaripour, M., Karimzadeh, I. et al. (2019). ‘Prebiotics: Definition, Types, Sources, Mechanisms, and Clinical Applications’, Foods, 8(3):92. Available at (Accessed 27 February 2024).

(11)Wastyk, H.C., Fragiadakis, G.K., Perelman, D. et al. (2021). ‘Gut Microbiota-Targeted Diets Modulate Human Immune Status’, Cell, 184(16), pp4137-4153.e14. Available at (Accessed 27 February 2024).

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