What chemo does to your gut microbiome and how to fix it

We know that chemo can cause diarrhea because it predominantly affects fast replicating cells like cancer cells, the gut cells, and hair cells. This is why many people experience diarrhea and hair loss during treatment. Unfortunately, the gut also contains this powerful collection of microbes collectively termed the microbiome (aka the gut flora). The microbiome refers to the numerous species of bacteria, viruses, fungi, and archaea that live within your GI tract, mostly residing in the colon. A healthy microbiome is a diverse ecology of all of these microbes that work in harmony with you, the host (1)!  At this moment, we are only beginning to understand the connections between the microbiome and human health.

Sadly for us chemo kids the microbiome is easily altered by drugs, most notoriously by antibiotics, but also by chemotherapeutics. So what does chemo do to our fragile bacterial ecosystem? Well one thing we know to be true is that chemo definitely causes a shit-storm (ooooh…weak pun, sorry)!

One study compared the bacterial composition of poop before and after chemo. What they found was that chemo dramatically shifted the type of bacteria in the gut and greatly reduced the bacterial diversity. Specifically, it increased numbers of “bad” bacteria like; Bactericides, Enterobacteriaceae, and Enterococci while reducing the numbers of “good” bacteria like, Bifidobacterium. They also noticed that the altered microflora after chemo helped create a more inflamed gut environment. This could make someone more vulnerable to infections or more likely to experience symptoms similar to those experienced in IBD (inflammatory bowel disease)(2,3).

So how do you fix your gut after getting ravaged by chemo? To be totally honest, we aren’t exactly sure. The science isn’t quite there yet for us to be certain but we do have some pretty good clues. Based on what we DO know, you should consume the following foods in order to rebuild and optimize a healthy microbiome:

High fibre foods: Fibre is fermented by gut bacteria into short chain fatty acids (SCFAs) which through complicated pathways help control inflammation and maintain a healthy gut environment (4,5). Eat a variety of fibre sources in order to best optimize your bacterial diversity (5,6). Great sources of fibre include: oats, barley, buckwheat, quinoa, brown rice, legumes, and whole fruits, and vegetables (1).

A mostly vegetarian diet (…with some good quality meats). According to a study in rural india, it’s best to include some meat in your diet in order to optimize your gut microflora. Caveat, this study was in rural india and likely does not represent a typical western omnivore diet (6). Also, it could be argued that excess protein and fat (like those found in animal meat) can be detrimental to the microbiome. So my take away? Eat mostly vegetarian.

Berries: Blueberries, strawberries, all the berries! These brightly coloured antioxidants were shown to increase bacterial diversity and numbers of “good” bacteria (6).

Nuts: Nuts and seeds have been correlated with an overall healthy diet, in particular pistachios seem to most enhance the microbiome. Consider adding in 1-3 servings of pistachios a day into your diet.

Probiotics: This may seem like a no brainer. Probiotics are great but unfortunately they aren’t yet a cure-all. Probiotics don’t actually colonize in the gut meaning those little microbes you swallow everyday don’t start to grow in your colon. However, probiotics do seem to change the type of bacteria present by promoting the “good” bugs and suppressing the “bad” bugs (3,5).

Eating raw or fresh fruits and vegetables: While raw is not necessary it does allow for more microbes to be present on and in the food you’re eating. Eating fresh rather than processed is another way of being exposed to more microbial diversity. Caution, eating fresh and raw food could expose you to more dangerous bacteria like salmonella and listeria, that can cause infectious diarrhea. In the grand scheme of risky things to do in life, I think I’ll risk it! (yup, I’m a wild child).

Fermented foods: Fermented foods like kimchi and sauerkraut are all the rage right now. While the evidence is lacking for if and how these foods impact the gut but there is reason to believe that due to the increased amount of bacteria in these foods they can alter the gut flora, short term. But if you eat them all the time I don’t see why these changes can’t be long term!

So how quickly can your gut microbiota change? Well it seems that within several days of following a new diet plan there can be changes in the microbiome(6). While most of these changes are in how the bacteria function rather than the makeup of the overall microbiome. Either way, these changes can still impact how you feel, the only thing that really matters.

So hopefully you can make something delicious with all the foods listed above!

I’ll be waiting for my dinner invite!

Bon Appetit!

Side note. I’ve used “good” and “bad” in quotations to simplify the very complicated science of intestinal microbiology. Since this science is still in its infancy, what little we do know is quickly translated into simpler marketing terminology like “good” and “bad” bacteria. All bacteria are neither good nor bad, they are integral parts in an ecology and that ecology needs to be fully intact and functioning as a whole in order to maintain health. We currently can only guess what components would make up an optimal microbiome (3).


(1) Harvie, R., Walmsley, R., & Schultz, M. (2017). “We are what our bacteria eat”: The role of bacteria in personalizing nutrition therapy in gastrointestinal conditions. Journal of Gastroenterology and Hepatology, 32(2), 352-357. doi:10.1111/jgh.13462

(2) Montassier, E., Gastinne, T., Vangay, P., Al-Ghalith, G. A., Varannes, S. B., Massart, S., . . . Knights, D. (2015). Chemotherapy-driven dysbiosis in the intestinal microbiome. Alimentary Pharmacology & Therapeutics, 42(5), 515-528. doi:10.1111/apt.13302

(3) Khoruts, A. (2017). Fecal microbiota transplantation–early steps on a long journey ahead. Gut Microbes, 8(3), 199-204. doi:10.1080/19490976.2017.1316447

(4) Grazul, H., Kanda, L. L., & Gondek, D. (2016). Impact of probiotic supplements on microbiome diversity following antibiotic treatment of mice. Gut Microbes, 7(2), 101-114. doi:10.1080/19490976.2016.1138197

(5) Mckenzie, C., Tan, J., Macia, L., & Mackay, C. R. (2017). The nutrition-gut microbiome-physiology axis and allergic diseases. Immunological Reviews, 278(1), 277-295. doi:10.1111/imr.12556

(6) Filippo, C. D., & Tuohy, K. M. (2015). A Nutritional Anthropology of the Human Gut Microbiota. Diet-Microbe Interactions in the Gut, 17-26. doi:10.1016/b978-0-12-407825-3.00002-2

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