Trillions of allies in your gut: how the microbiome affects cancer treatment

Basics

What the microbiome actually is

The gut microbiome is an ecosystem of trillions of bacteria, fungi, viruses, and other microorganisms living in your digestive tract. They exchange signals with one another, respond to food and the surrounding environment, and maintain a stable internal balance (homeostasis). Scientists now call the microbiome a "virtual organ" — because although it isn't an anatomical organ like the liver or kidneys, it performs many vital functions that would otherwise require one. The microbiome complements human physiology by carrying out metabolic functions the human body has no enzymes of its own for.

Our bodies lack the enzymes to break down many plant fibers. That's where gut bacteria step in: they ferment dietary fiber and produce short-chain fatty acids (SCFAs) — butyrate, acetate, propionate. Butyrate, for example, is the main fuel for the cells lining the colon and has a strong anti-inflammatory effect. It's also involved in synthesizing vitamin K and some B vitamins, in bile acid metabolism, and in breaking down various nutrients and medications.

The microbiome also regulates your immune system. How, you might ask? Pay attention here. A significant portion of the body's immune cells live not just anywhere, but specifically in the gastrointestinal tract (your digestive system). The microbiome trains the immune system starting right after birth. It supports the development of regulatory T-cells — a type of immune cell that acts as a "brake" on the immune system. They stop the body from overreacting and help limit unnecessary inflammation. The microbiome also protects against colonization by pathogenic microorganisms. As you can see, without a normal microbiome, the immune system functions significantly less effectively.

There's also what's known as the gut-brain axis. Bacteria influence the metabolism and signaling pathways related to: serotonin (the chemical messenger involved in regulating mood, sleep, appetite, and even gut motility), GABA (the substance that helps calm the nervous system), dopamine (which gives us motivation, reward, learning, and movement control), the short-chain fatty acids we already mentioned, as well as numerous signaling molecules. Communication between the gut and the brain travels through: the vagus nerve (the longest nerve in the human body — it connects the brain to many internal organs and acts as a "communication highway"), the immune system, hormones, and microbial metabolites. So what's actually happening in your gut can affect: your mood, your stress response (yes, that exact moment when you freeze and don't know what to do), your sleep (the same sleep you keep putting off for "just one more" video on your phone), your appetite, and your cognitive function (how well your brain works).

The microbiome also protects the body by competing for nutrients. Picture your gut as a well-organized neighborhood. When it's populated by beneficial bacteria, all the "spots" are already taken and the food is divided among them. If disease-causing microorganisms show up, there's almost no room and no resources left for them to settle and multiply. Beneficial bacteria also release substances that block the growth of unwanted microbes and help keep the gut barrier healthy — they help keep the gut wall strong and tight, so harmful microorganisms and toxins can't easily cross into the bloodstream.

And if all of that wasn't enough to convince you of its uniqueness — here's one more thing: the microbiome is also a huge "genetic organ." The human genome contains around 19 to 20,000 genes. By comparison, the combined genome of the gut microbiome includes millions of genes — roughly 100–150 times more than the human genome, according to classic estimates, though the exact number varies between individuals and studies. All of those extra genes provide metabolic capabilities the human body doesn't have on its own.

Its composition takes shape from birth and stabilizes in adulthood. High microbial diversity marks a healthy state. Dysbiosis — the disrupted balance, is linked to inflammation, metabolic disorders, and a poorer response to treatment.

Science

The link to treatment — what the science shows

Here's something few people expect: the composition of your gut microbiome before treatment even starts may be linked to how well your body responds to therapy.

For example, a large study published in 2022 in Nature Medicine followed patients with advanced melanoma treated with immunotherapy. The researchers found that patients with a more diverse and balanced gut microbiome were more likely to respond successfully to treatment. These patients more often had bacteria associated with a diet rich in fiber and omega-3 fatty acids.

In my own research, focused on patients with gastrointestinal tumors on immunotherapy, the picture is similar: a high intake of dietary fiber (≥20 g/day) was associated with a higher objective response to treatment and longer survival. These patients also had more bacteria (such as Faecalibacterium prausnitzii, Akkermansia muciniphila, and Ruminococcaceae) that support the activity of immune cells (CD8+) responsible for recognizing and destroying tumor cells.

Of course, science is still searching for final answers. Not every patient responds the same way to treatment, and the microbiome is just one of many factors. But unlike age, genetics, or tumor type, the microbiome is a factor we can influence, to some extent, through diet and lifestyle. That's exactly why it's becoming an increasingly important topic in modern oncology.

Mechanism

What actually happens during chemotherapy

Research on the microbiome and immunotherapy is the most extensive, but chemotherapy affects the gut microbiome in its own, very direct way.

Chemotherapy drugs attack rapidly dividing cells — including the ones that make up your gut lining. The result is often mucositis — inflammation of the mucous membrane that can affect the mouth, esophagus, stomach, and intestines.

When the gut lining is damaged, the intestine's protective barrier weakens. This makes it easier for bacteria and their byproducts to cross the gut wall into the bloodstream — a process known as bacterial translocation. In people with a weakened immune system, this raises the risk of infection and can require antibiotic treatment, or even delaying the next round of chemotherapy.

At the same time, many patients receive antibiotics — either preventively or because of an infection that's already occurred. While sometimes life-saving, antibiotics can wipe out not only harmful bacteria but also some of the beneficial ones, further disrupting the microbiome's balance.

This combination — a damaged gut barrier, an altered microbiome, and weakened immune defenses, is one of the reasons symptoms like diarrhea, bloating, abdominal pain, nausea, and a higher risk of infection often show up during chemotherapy.

The good news is that eating in a way that supports the gut microbiome can be a valuable ally during this period. It can't prevent every side effect and doesn't replace treatment, but it can help maintain the gut barrier, support the recovery of beneficial bacteria, and, in some patients, ease some gastrointestinal symptoms. That's exactly why more and more current research treats the microbiome as an important part of supportive care during cancer treatment.

Protocol

What to eat for gut health

Fiber — the foundation

The target, backed by the research above, is at least 20 g of fiber a day, when your condition allows it (with severe diarrhea or bowel stenosis, this recommendation may change — follow your care team's guidance).

Good sources: oats, beans and lentils (well-cooked, easy to digest), brown rice, pears, apples with the skin on, carrots, steamed broccoli, Brussels sprouts.

In practice

8 meal ideas to easily reach 20–30 g of fiber a day

Distinction

Prebiotic foods — "food for the good bacteria"

Not all fiber is the same — prebiotic foods, for instance, contain a special type of fiber that isn't broken down by the human body but selectively feeds beneficial bacteria: garlic, onion, leeks, asparagus, slightly green bananas, barley, rye, beans, lentils, chickpeas, chicory, and Jerusalem artichoke. You don't need large amounts at once — even small portions, eaten regularly, can gradually help beneficial gut bacteria develop.

Eating model

Mediterranean, not Western

The research is consistent on one point: how we eat day to day has a powerful effect on the gut microbiome. The Western eating pattern — low in fiber but high in sugar, saturated fat, and ultra-processed foods, is associated with reduced diversity of beneficial bacteria, dysbiosis, and chronic low-grade inflammation. A growing number of studies suggest this kind of microbiome profile may also be linked to a weaker response to some anti-cancer therapies.

This eating pattern doesn't just nourish you — it also feeds the beneficial bacteria in your gut, which in turn produce anti-inflammatory substances and help maintain a strong gut barrier.

What does this look like in practice?

You don't need to change everything at once. Small, consistent changes can make a difference. For example:

• choose oats instead of sweetened cereal
• add a serving of legumes a few times a week
• use olive oil instead of butter to dress salads
• swap some red meat for fish or legumes
• include vegetables in at least two meals a day

Your diet doesn't need to be perfect. The microbiome doesn't expect perfection — it responds to what you do consistently. Even small changes, once they become habits, can gradually support a more diverse and healthier gut microbiome.

Remember: there's no single "superfood" for the microbiome. Diversity matters most. The more different plant foods you have in your diet over the course of a week, the more different types of beneficial bacteria can be fed. That diversity is considered one of the most important markers of a healthy gut microbiome.

A note of caution

Fermented foods

Fermented foods contain beneficial microorganisms that can help support the diversity of your gut microbiome. The best studied are yogurt with live cultures and kefir, but the group also includes sauerkraut, kimchi, and a number of other traditionally fermented foods.

It's worth knowing that fermented foods aren't a "medicine" for the microbiome. The greatest benefit is seen when they're part of a broader diet rich in varied plant foods and fiber. In fact, beneficial bacteria need not only to be consumed but also to receive the right "food" — prebiotic fiber, so they can establish themselves and thrive in the gut.

Practical tip: if you have no contraindications, a cup of kefir or a serving of yogurt with live cultures, combined with oats, fruit, or flaxseed, is far more beneficial for the microbiome than fermented food on its own. That way, you provide both beneficial bacteria (probiotics) and food for them (prebiotics) — a combination that supports their growth.

Safety

An important warning about probiotic supplements

I need to be direct here, because it affects your safety directly. When people talk about the microbiome, many first think of probiotic capsules — supplements containing concentrated amounts of live microorganisms. It's important to know, though, that "beneficial" doesn't automatically mean "appropriate at every point in treatment."

In patients undergoing active chemotherapy, especially with neutropenia, probiotic supplements should be discussed with the care team. The reason is that two things can happen at once during treatment: chemotherapy, as mentioned, can damage the gut lining and disrupt the intestine's natural protective barrier, and neutropenia reduces the body's ability to control microorganisms, even ones normally considered safe.

What does this mean in practice? Not all microbiome-related products are the same:

These are different categories of products and shouldn't automatically be treated as interchangeable.

Supporting the microbiome doesn't necessarily mean taking supplements. In many cases, the safest approach is to first focus on your eating pattern — enough fiber (when appropriate), a variety of plant foods, and nutrition tailored to your individual situation during treatment.

Frequently asked

A quick word on the ketogenic diet and the microbiome

When it comes to diet and cancer, the ketogenic diet often comes up — an eating pattern very low in carbohydrates, moderate in protein, and high in fat. This diet draws interest in oncology because it changes how the body uses energy — it lowers blood glucose and pushes the body to produce ketone bodies as an alternative energy source.

In theory, this could affect some tumors, since many cancer cells prefer to use glucose as their main energy source (more on this in our article: "Sugar and Cancer — Myth or Reality"). The reality, though, is more complicated. The scientific data show that the effect of a ketogenic diet can depend on the type and biology of the tumor, the stage of disease, the patient's overall condition, the type of anti-cancer treatment, and the individual composition of the gut microbiome.

In some tumor models, researchers are studying whether restricting carbohydrates can affect tumor cell metabolism, autophagy (a "cellular recycling" process), and the activity of certain immune cells, including T-cells. But in other situations, the effect can be different — some tumor cells can adapt to the changed nutritional environment and use other energy sources, including ketone bodies. This means there's no single diet that works the same way across every type of cancer.

From a microbiome perspective, the ketogenic diet isn't clear-cut either. When carbohydrates and plant foods are heavily restricted, fiber intake often drops too — the main "food" for beneficial gut bacteria. That can shift the microbial balance.

During cancer treatment, the main goal of nutrition usually isn't to shift a single metabolic pathway — it's to help the body preserve strength, muscle mass, immune function, and the ability to get through therapy.

This article is for educational purposes and doesn't replace consultation with your treating physician or dietitian. Recommendations for fiber, fermented foods, and especially probiotic supplements need to be weighed against your current blood counts and the specific stage of your treatment — always check with your oncology team, particularly if you have neutropenia.

Sources

1. Tini, S. et al. Diet, gut microbiota and immunity across the cancer continuum. Nutrients, 17, 2898 (2025).
2. Simpson, R.C., Shanahan, E.R., Batten, M. et al. Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome. Nature Medicine, 28(11), 2344–2352 (2022). — doi.org/10.1038/s41591-022-01965-2
3. Bogdanova, A.-M., Hadzhieva, S. The modifiable link: diet, microbiome, and therapeutic response in immunotherapy for GI tumors. Original research, awarded first place at a student scientific session, Medical University "Prof. Dr. Paraskev Stoyanov" — Varna.
4. Spencer, C.N., McQuade, J.L., Gopalakrishnan, V. et al. Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response. Science, 374(6575), 1632–1640 (2021).
5. Bolte, L.A., Lee, K.A., Björk, J.R. et al. Association of a Mediterranean diet with outcomes for patients treated with immune checkpoint blockade for advanced melanoma. JAMA Oncology, 9(5), 705–709 (2023).
6. Somodi, C., Dora, D., Horváth, M. et al. Gut microbiome changes and cancer immunotherapy outcomes associated with dietary interventions: a systematic review. Journal of Translational Medicine, 23(1), 756 (2025).
7. The efficacy and safety of probiotics in people with cancer: a systematic review. Annals of Oncology. — www.annalsofoncology.org/article/S0923-7534(19)36598-6/fulltext
8. Beckerson, J., Jones, N., Lodhia, S. et al. Dietary advice during neutropenia: An update and consensus from the Haematology subgroup of the BDA Oncology Group. Complete Nutrition, 12(6), 40–42 (2012).
9. Elkrief, A. et al. Gut microbiome and resistance to cancer immunotherapy. Nature Reviews Drug Discovery (2025).