The Ultimate Guide to Optimising Cancer Outcomes Through Microbiome Modulation
Cancer care is evolving and so is our understanding of what truly supports optimal outcomes for our patients. One of the most exciting and rapidly expanding areas of research is the role of the gut microbiome in cancer development, treatment response, and recovery.
The human microbiome does more than aid digestion. It influences inflammation, immunity, nutrient metabolism, and even how a patient responds to chemotherapy and immunotherapy. As clinicians, we now have the opportunity and responsibility to consider microbiome health as a core part of integrative cancer care.
Whether you're supporting a patient through chemotherapy, preparing someone for immunotherapy, or working to rebuild gut health post-treatment, this guide will walk you through the evidence and give you practical tools to improve outcomes and quality of life.
How the Gut Microbiome Influences Cancer Risk and Progression
The gut microbiome plays a significant role in cancer development and progression. From modulating inflammation to influencing the immune system and even impacting how drugs are metabolised.
A Consistent Pattern: Colon Cancer
While research is still emerging across many cancer types, the most consistent and well-studied link is with colorectal cancer. Numerous studies have identified a clear microbial signature, including increased levels of oral-derived pathogens like Fusobacterium nucleatum and Parvimonas micra, and a reduction in beneficial SCFA-producing species like Roseburia intestinalis. These microbial shifts are associated with chronic low-grade inflammation, mucin layer degradation, and alterations in amino acid metabolism—all of which contribute to tumour initiation and progression.
Fun Fact:
In microbiome research, it’s rare to see consistent patterns, but in colon cancer, about 75% of studies report similar microbial shifts.
Patients with colon cancer tend to have:
A rise in oral microbes (like Fusobacterium nucleatum and Parvimonas micra) these don’t belong in the gut!
Increased mucin and amino acid degradation, which can compromise the gut barrier and fuel inflammation.
A decline in fibre-fermenting species and pathways, which
reduces production of beneficial
short-chain fatty acids (SCFAs).
Clinical Pearl:
An overgrowth of oral microbes in the gut often reflects poor stomach acid or oral health issues worth assessing in patients with gastrointestinal cancers.
But What About Other Cancers?
In breast, lung, prostate, and blood cancers, the microbial patterns are far more variable. No clear “microbial signature” has emerged across all types. However, we are beginning to see trends: for example, low levels of fibre-fermenting bacteria and high levels of pro-inflammatory species are frequently associated with poorer treatment outcomes across many tumour types. In lung and breast cancer, the presence of oral bacteria in the gut, has been linked to reduced response to immunotherapy.
Clinical Pearl:
Even without a universal microbial fingerprint, supporting SCFA production, protecting gut lining integrity, and avoiding dysbiosis remain key strategies across all cancer types.
Gut Microbiome and Cancer Treatment: What Affects Chemo and Immunotherapy Outcomes
When it comes to cancer therapy, not all patients respond equally and the gut microbiome is emerging as a key factor in that variability. Whether your patient is undergoing chemotherapy or immunotherapy, the composition of their gut microbiome can help or hinder treatment effectiveness.
Chemotherapy: Friend or Foe? Depends on the Microbes
Chemotherapy works by targeting rapidly dividing cells, but certain microbes in the gut can literally interfere with drug activity. Researchers have identified that some bacteria particularly Gammaproteobacteria and Fusobacterium nucleatum can deactivate chemo drugs, making them less effective.
Clinical Pearl:
Before starting chemo, test for Fusobacterium nucleatum and Gammaproteobacteria. If present, consider:
Prebiotic interventions like GOS (4g/day) and HMOs (2g BID),
Reducing saturated fats, which fuel Gram-negative and pro-inflammatory microbes.
Immunotherapy: The Microbiome as an Immune Ally
Immune checkpoint inhibitors (like anti-PD-1 drugs) are game-changers but their effectiveness can be amplified or reduced by the gut microbiome.
Studies show that:
SCFA producers and fibre fermenters are enriched in responders.
Pro-inflammatory and oral species are more common in non-responders.
High levels of Akkermansia muciniphila are associated with worse outcomes, especially if >4.8% relative abundance.
Clinical Pearl:
Before immunotherapy, test for:
SCFA-producing species
Oral microbes
Akkermansia muciniphila
The Antibiotic Alarm Bell
Here’s where things get urgent. Repeated studies show that antibiotic use even up to 12 months before cancer treatment can significantly reduce treatment response and survival outcomes.
Fun Fact:
A meta-analysis of over 41,000 immunotherapy patients found antibiotics were consistently associated with worse overall survival.
Clinical Pearl:
If your patient truly needs antibiotics, protect their microbiome:
Prescribe HMO (2g BID) to feed beneficial microbes
Use Saccharomyces boulardii + BB12 where appropriate
Load up on prebiotic fibre (RS, PHGG, FOS) before, during, and after the course
Essential Microbiome Markers to Assess in Oncology Patients
As practitioners, we often ask: “What should I be looking for on a microbiome test when my patient has cancer?” The answer? Not just one thing but a pattern of features that can help guide your interventions, reduce treatment side effects, and improve outcomes.
Here are the top microbiome metrics to assess before, during, and after cancer treatment.
1. Specific Microbial Species (Not Just Diversity!)
We tend to think “more diversity = better health,” and while that’s generally true, when it comes to treatment response, it’s specific species that matter most.
What to look for:
Fusobacterium nucleatum
Gammaproteobacteria
Akkermansia muciniphila
SCFA producers like Roseburia intestinalis, Faecalibacterium prausnitzii
Clinical Pearl:
High levels of F. nucleatum or Gammaproteobacteria = possible chemo resistance. Low SCFA producers = poor treatment response. High A. muciniphila = immunotherapy red flag.
2. Inflammatory Potential
Look for signs of:
Hexa-LPS producers (endotoxin-forming Gram-negative bacteria)
Oral species in the gut (e.g., Parvimonas micra, Peptostreptococcus stomatis)
These microbiome don’t just sit around they drive inflammation, degrade mucin, and promote tumour progression.
3. SCFA Production Pathways
SCFAs like butyrate, acetate, and propionate are key players in immune regulation, gut barrier integrity, and inflammation control.
What to check:
SCFA-producing pathways (via functional metagenomics)
Abundance of fibre-fermenting species
Clinical Pearl:
Low SCFAs? Time to load up on prebiotic fibres like resistant starch, beta-glucan, and PHGG. These are critical for treatment response especially for immunotherapy patients.
4. Mucin Degradation Activity
Excess mucin-degrading microbes = compromised gut barrier + higher inflammation risk.
Check for:
Elevated mucin degradation pathways
High levels of bacteria like Akkermansia muciniphila (especially if the patient is fibre-deficient)
Clinical Pearl:
Pair mucin-degraders with dietary patterns. Fibre-poor diets drive these microbes. Whole grains can reverse the trend and support SCFA production.
5. Presence of Pathogens or Pathobionts
In cancer patients, especially those undergoing chemo new-onset GI symptoms are often under-investigated. Yet up to 20% of diarrhoea cases are linked to detectable pathogens.
Fun Fact:
The latest expert guidelines recommend comprehensive stool testing (not just PCR panels) in cancer patients with acute diarrhoea. In clinical practice I use MetaPanel which can detect 175 pathogens.
Clinical Pearl:
If you detect a pathogen, treat it but protect the microbiome at the same time. Use microbiome-safe antimicrobials and co-prescribe supportive fibres and probiotics where indicated.
6. Overall Diversity and Resilience
While diversity doesn’t strongly predict treatment response, it does predict side effects like:
Infection risk
GI toxicity
Febrile neutropenia
Clinical Pearl:
Patients with lower Shannon Index diversity are 4x more likely to develop infections after chemo. Boost diversity with polyphenols, diet variety, and fermented foods.
Pathogen Screening in Cancer Patients: When and How to Test the Gut
When a cancer patient develops gastrointestinal symptoms during treatment like diarrhoea or bloating it’s easy to assume it’s just a side effect of chemotherapy or immunotherapy. But that assumption could be costing them recovery time, resilience, and even treatment success.
Here’s what practitioners need to know about pathogen detection in oncology patients, and how to manage these cases with precision and care.
GI Symptoms? Don’t Just Guess—Test!
Up to 20% of cancer patients with new-onset diarrhoea during treatment actually have a detectable pathogen. Yet stool testing is often skipped or limited to basic PCR panels and only measure 5–10 pathogens. In clinical practice I use MetaPanel which can detect 175 pathogens.
Fun Fact:
A 2025 international panel of experts recommended comprehensive stool testing for all cancer patients who develop acute diarrhoea not just those who are neutropenic.
Clinical Pearl:
Look beyond C. difficile. Many patients with cancer-related diarrhoea have non-classical pathogens like Campylobacteror Cryptosporidium some of which are self-limiting and don’t require antibiotics.
Balancing Eradication & Preservation
Yes, you may need to treat. But if you do, protect the microbiome at the same time.
If antimicrobial treatment is required:
Use narrow-spectrum options if possible
Co-prescribe HMO (2g BID) helps feed beneficial species and reduce pathogen adhesion
Include S. boulardii + B. animalis (BB-12) to protect diversity
Support with targeted prebiotics (resistant starch, beta-glucan, PHGG, FOS)
Re-test after treatment to assess recolonisation
Clinical Pearl:
Many herbal antimicrobials also damage the microbiome avoid these during active cancer treatment unless absolutely necessary.
When to Test for Infections in Cancer Patients
Use this as a clinical checklist for stool testing:
Test Stool In Cancer Patients With:
Acute diarrhoea (new or worsened)
GI symptoms persisting >3 days
Mucous or blood in stools
Fever + GI symptoms
Immunocompromised state
Recent travel or hospitalisation
History of antibiotic use
Top 5 Microbiome Strategies to Improve Cancer Treatment and Reduce Side Effects
Now that we know what to look for, let’s dive into what we can actually do. Microbiome modulation in cancer care isn’t about trendy supplements or guesswork it’s about targeted, evidence-informed strategies that support gut integrity, immune function, and treatment response.
Here are the five core strategies every practitioner should know when working with oncology patients.
Increase Short-Chain Fatty Acids (SCFAs)
SCFAs—especially butyrate, acetate, and propionate are powerhouse molecules produced when gut bacteria ferment fibre. They:
Fuel colonocytes
Regulate immune activity
Reduce inflammation
Improve treatment response, especially in immunotherapy
Top Prebiotics for SCFA Production:
Resistant Starch (RS): 10g twice daily
Beta-glucan: 3.5g twice daily
PHGG (Partially Hydrolysed Guar Gum): 10g daily
Human Milk Oligosaccharides (HMOs): 2g twice daily
Pectin: typically 3g twice daily
Fructooligosaccharides (FOS): 5g twice daily
Fun Fact:
Higher daily fibre intake (≥20g/day) has been linked to improved survival in immunotherapy patients.
2. Improve Microbial Diversity
While diversity doesn’t directly influence treatment response, it’s protective against chemo side effects.
How to Boost Microbial Diversity:
Eat the rainbow – 30+ plant types/week
Rotate proteins – fish, legumes, pastured eggs, nuts
Fermented foods – sauerkraut, kefir, tempeh
Herbs & spices – cumin, turmeric, basil, ginger
Polyphenols – berries, green tea, cacao, olive oil
Clinical Pearl:
Diversity is more than variety it’s resilience. Encourage patients to try one new food every week to build breadth in the diet and microbiome.
3. Reduce Mucin Degradation
Excess mucin-degrading microbes erode the gut’s protective lining, increasing susceptibility to pathogens and inflammation.
Common culprits:
Low fibre diets
Overgrowth of A. muciniphila (in high levels)
Refined grain-heavy meals
Your Solution:
Emphasise whole grains over refined carbs
Boost fibre-rich foods (especially prebiotic types)
Rebuild with SCFA-producing bacteria
Clinical Pearl:
A wholegrain diet has been shown to increase SCFA pathways, and reduce mucin-degrading enzyme activity all within weeks
4. Reduce Oral Species in the Gut
When oral microbes show up in the colon, they’re not harmless hitchhikers. They’re associated with:
Colon cancer
Poor immunotherapy response
Inflammatory signalling
Strategies to Reduce Oral Microbes:
Improve stomach acid – use betaine HCl, herbal bitters
Support vagus nerve – meditation, breathwork, gut hypnotherapy
Prioritise oral hygiene – flossing, probiotic rinses
Targeted probiotics – L. helveticus, B. longum, S. boulardii
Fun Fact:
Stress can drive oral bacteria to overgrow in the gut yoga might be as important as probiotics in these cases.
5. Protect the Microbiome During Antibiotic Use
If your patient needs antibiotics during cancer care (e.g., for neutropenic fever), your job is to minimise collateral damage to the microbiome.
Protective Co-Prescriptions:
HMO (2g twice daily) – feeds beneficial bacteria, reduces pathogen adhesion
S. boulardii + BB12 (10B CFU) – supports microbial balance
Prebiotics – RS, PHGG, FOS, beta-glucan
Bonus Tip:
Also apply these principles if using antimicrobial herbs many are equally disruptive and should be used sparingly or avoided altogether during treatment phases.
Clinical Summary: How to Support Cancer Patients Through Microbiome Modulation
As our understanding of the gut microbiome deepens, so does our ability to influence cancer outcomes in meaningful ways. The evidence is clear: the microbiome is not just a bystander in oncology it’s an active participant in how patients respond to treatment, experience side effects, and recover.
For practitioners, this means moving beyond general gut support and toward targeted microbiome-informed care. By testing, identifying, and modulating key microbial patterns, we can support:
Improved chemotherapy and immunotherapy responses
Reduced GI and immune-related side effects
Better patient resilience during and after treatment
Practitioner Takeaways:
Test strategically: Focus on SCFA producers, mucin degraders, oral species, and pathogens, not just overall diversity.
Modulate wisely: Use fibre, food, prebiotics, and selective prebiotics to shape the terrain.
Protect intentionally: Avoid unnecessary antibiotics and antimicrobials, and always support the gut if they’re used.
Above all, remember: cancer treatment is tough on the body. If we can support the microbiome, we support the whole person enhancing not just their clinical outcomes, but their quality of life.
Dr Brad Leech
Brad is a PhD-qualified Clinical Nutritionist and Herbalist specialising in chronic autoimmune conditions and complex gastrointestinal disorders. He provides complete and personalised care to his patients using functional nutrition, integrative medicine and holistic wellness.