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Microbiome: We are mostly human


In this article Dr Carol Granger, focuses on the wonders of our microbiome and its important influence on our health.

We are mostly human. (Or, “it’s life Jim, but not as we know it”)

Allow me to introduce you to your microbiome. Inside the digestive system is a collection of many millions of microbes, these can add up to around a kilo in a typical adult, and these have an important influence on health. Now if that sounds a bit too ‘icky’ just imagine them as a couple of tubs of yoghurt.

The human microbiome is spread throughout the body, and in each location there will be differences in the range and proportions of species of microbes present. Imagine each is a separate niche with its own conditions. So the pattern of microbes in the mouth will be different to those in the nose and lungs.

The ‘gut microbiome’ spread throughout the digestive system has some of theMicrobiome in our gut species from the mouth, but also considerable variation at different parts of the bowel. The bladder and genital tract, and the skin also provide niches for the microbiome.

We acquire the microbiome at birth, from our mothers during the birth process itself and by the very first skin contact. From the first breath, we are acquiring bacteria, from everything that goes into our mouths food and all of the external exposures.

What is a healthy microbiome and how do we get it?

A ‘healthy’ microbiome is considered to be one with a broad array of species, with some particular species that may be more beneficial, and some species that appear to be less helpful. Food has the most obvious influence on microbe composition, and some very elegant studies have explored this.

Studies with people from different cultural backgrounds and diets have looked at swapping their diets for short periods of time. It takes only a few weeks for the change in diet to have an effect on the microbiome! In general, a more processed diet typical in the ‘industrialised world’ is associated with less microbial diversity and an overall less healthy microbiome.

So what’s the significance of this mass assembly of microbes for our health? Far from being silent passengers, they are vital for our existence, but they can also spell trouble. Some inhabitants of the microbiome can be disease causing if left unchecked.

It is now understood that various species of microbes in the microbiome communicate with the immune system using biological signals. One of the main mechanisms of this interaction is via the blood cells circulating in the walls of the intestine where they come into close contact with the gut microbiome.

It’s been suggested that very early exposures have a major influence on immunity. There are many aspects of modern life that have a negative effect on the microbiome, including alcohol, stress, smoking, antibiotics and other medication, to name a few. Even your choice of soap can have an effect!

Our microbiome, our immune system and diet

Some recent studies with people receiving new immune therapy cancer drugs suggested that the microbiome may have quite profound influences. Researchers exploring the variation in response to these drugs have been studying the dietary intakes and samples of faeces from patients on these drugs (1). These are early studies, with more research needed, but it seems that the best responses to these drugs were seen in people with the most diverse microbiomes. A healthy microbiome may be internal ‘boot camp’ for the immune system.

Much more research is needed to understand these mechanisms and how they can be optimised. A plant-based diet which provides several types of fibre supports the growth of beneficial microbes, and this may play a part in responding well to these treatments.

This may be helpful in many other ways, not just for people receiving immunotherapy. Many different research groups are looking at the microbiome and its influence on health, and it’s becoming apparent that a broad diverse microbiome is associated with better health in many other ways too, not only related to cancer.

So it seems a sensible strategy, unless you have medical advice to the contrary,Plate of plat based food to include fibre-rich foods in your diet. Some foods are good
at supporting beneficial microbes, these are prebiotic foods and they include vegetables, fruits, whole grains, nuts, seeds and especially mushrooms. Other foods contain beneficial microbes, these are probiotic foods such as yoghurt and kefir with live cultures, and other cultured foods like sauerkraut.

One aspect of cancer diets that will doubtless receive more attention soon, is how dietary components can influence this ‘microbiome’ in people affected by cancer, and having various treatments.

A few notes of caution, live cultures in foods can present a risk to people with very low white blood cell counts and especially neutropenia, so follow your medical team’s advice in that regard. When you need to avoid live cultures, then prebiotic foods are a safe way of supporting your microbiome in those circumstances of immunosuppression.

Secondly, a high fibre diet may not suit everyone, and with your microbiome, more doesn’t always mean better. It’s good to have a wide range of plant foods, even if it’s just a small amount of each one. You may need to have a low-residue diet for a time after treatment such as bowel surgery.

Ask your clinical team how long you are expected to be following a low residue regime, as low residue is low fibre, and that means low levels of nutrients for your beloved microbiome.

Making your own fermented foods

Finally, if you are tempted by the many online resources to make your own fermented foods, there are some risks that are worth noting, especially in people with compromised immunity. Spoilage organisms may inadvertently sneak into your culture from air, water, containers, and from foods being prepared for culturing.

Common ‘spoilage organisms’ do as their name suggests, they spoil the taste and texture, and are often detectable from the smell or taste of the food. More sinister guests can invite themselves to dwell in your cultured foods, such as:

  • Clostridium botulinum, the cause of botulism, a particularly nasty and often fatal form of food poisoning.
  • Listeria monocytogenes, also reported as an unintended consequence of home preserved and fermented foods (2).

These are risks for anyone, but particularly for those living with a health condition, especially when you may have a compromised immune system. Enjoying a reputable commercial brand of cultured foods is a wise move, and always take heed of your clinical team’s advice on whether you able to eat food with live cultures.

So, when planning your next meal spare a thought for your inner inhabitants, and remember that we’re only mostly human.


(1.) Yi, M., Yu, S., Qin, S., Liu, Q., Xu, H., Zhao, W., & Wu, K. (2018). Gut microbiome modulates efficacy of immune checkpoint inhibitors. Journal of haematology & oncology, 11(1), 47.
(2.) Medina, E., de Castro, A., Romero, C., Ramírez, E. M., & Brenes, M. (2016). Safety of fermented fruits and vegetables. In Regulating Safety of Traditional and Ethnic Foods (pp. 355-367). Academic Press.


Dr Carol Granger, DProf MSc, is a registered nutrition practitioner who works with people with a cancer diagnosis. Before her career in nutrition, she worked in biosciences, including as a microbiologist and biochemist. She has a particular interest in the world of the microbiome, the impact of nutrition and lifestyle on its composition, and its interactions with immunity.

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