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Category: Science


Chemotherapy and the Microbiome

I’ve been receiving a lot of questions lately about the effects of chemotherapy on the gut microbiome. What I’ve discovered is that there is, in fact, very little literature that explores this information. In reading that, we must recognize that about 90% of all the published literature dealing with the microbiome has been published only in the last 5 years.

Chemotherapy as a term actually encompasses a broad array of interventions. Various chemotherapeutic agents are used to target particular diseases. Related to cancer in general, about 650,000 Americans get chemotherapy, in one form or another, each year.

One recent study, looking at the effects of chemotherapy on the microbiome, evaluated patients who were receiving chemo to prepare them for stem cell therapy. These were patients with a form of blood cancer called non-Hodgkin’s lymphoma.

Basically, the technique involves administering a powerful chemotherapeutic agent that wipes out the cancerous bone marrow, so that a bone marrow transfer of stem cells can then be performed in hopes of repopulating the bone marrow with healthy cells.

Typically, when the chemotherapy agent is administered, there is irritation of the gut (mucositis), and, likely, this is what provoked the researchers to study the microbiome of these individuals.

The study looked at the genetic signatures of the gut bacteria of 28 patients both before and after chemotherapy. None of the subjects received antibiotics.

The authors found that chemotherapy had a dramatic effect on the gut organisms, stating in their conclusion:

In summary, we found a profound disruption of the intestinal microbiome in terms of both taxonomic composition and metabolic capacity that may partly explain the acute inflammation, known as GI mucositis, observed after chemotherapy. This dysbiosis is also characteristic of other acute and chronic inflammatory conditions in mice as well as in humans, suggesting a causal role for the microbiome in chemotherapy-induced GI mucositis.

In addition, the report described significant changes in energy metabolism and even the ability of the gut bacteria to participate in producing important metabolic co-factors like vitamins. So as it relates to the microbiome, there may well be long term and significant health consequences of chemotherapy that have not yet even been considered. As always, we need to look at the risk/benefit ratio of any medical treatment, as countless lives have been saved by aggressive treatments such as that described.

But moving forward, it might be reasonable to consider some form of gut preservation techniques, like recolonization, following an intervention like chemotherapy, now shown to have such a profound effect on the microbiome. Just as these patients received stem cells to repopulate their bone marrow, perhaps fecal transplantation would be appropriate to repopulate their intestines.

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  • TechnoTriticale

    Where might one find a protocol for autologous FMT?

    • Lynn Dell

      For a cancer patient, prior to getting chemo and radiation? Perhaps the cancer itself would disturb the microbiome and it might be better to have a FMT from a source who is healthy, optimal weight, etc..

      • Yvonne Forsman

        I seriously doubt there are any healthy ppl in the US. Our food is polluted, water is polluted, air is polluted. My best guess would be FMT transplant from countries like Bolivia or Russia who prohibit GMO.

        • Ash Jafri

          Dear Doctor Perlmutter,
          I was wondering why some one in Microbiology does not study and come up with an intravenous injection to introduce, GOOD BACTERIA and devise a method to actually determine a person’s present storage and what dosage a person will require to full fill the need for an optimum amount. Probably there is a range depending on the age, diet and perhaps many other factors
          Do we know the rate of depletion, besides getting knock down by Antibiotics. Do we know the effects of other medication, anxiety, abnormal brain function etc;
          Ash Jafri. RSVP.

          • Ruth Griffith

            i think you have made a good point i would like to know this also ill research this

        • Ruth Griffith

          your right and that is why they say buy from places that are very poor because they dont have money to be buying chemicals to load into our fod and water and everything . it is best to boil your water before u drink it then drink only two thirds of the water then pour the rest out then look at the bottom of your pot and see if you see a white looking color if u do it is bleach that is used in our water supply

  • Merry Spirit

    Seems to me a person with a healthy microbiome would be less ikely to develop cancer in the first place.

    • Yvonne Forsman

      Most foods in the grocery store have been grown with the use of chemicals in our big scale agriculture system. Chemicals, especially Glyphosate (Roundup) is a known carcinogen. 1 in 3 men and 1 in 2 women will get a cancer diagnosis. If you shop only organic and filter your water and air, and never get vaccines, you may be healthy and not get cancer. Do you know at least one single person fitting this description? I don’t.

    • Ruth Griffith

      all people have good and bad bacteria in their bodies and they have to get rid of the bad by detox the body so the body can heal . see some times people get cancer from eatting meat because the animal is fed harmones and antbotic s and that gives them cancer then the animal is killed and sold in the stores , we buy the meat we then get cancer too and it starts by damaging our dna then it breaks loose and that is called free radicals .

  • enubus

    How about cortisone therapy in Prostate Cancer? Does that effect the microbiome? He had radiation a number of years ago for the same diagnosis and 9 years later it came back. He has had bowel difficulties ever since. What would you recommend nutritionally, he is 89 and quite active.

    • Yvonne Forsman

      If he lives in a state where medical cannabis is legal then Rick Simpson oil is known to battle any cancer. He would need 1. google doctors who are authorized to approve his cancer for medical marijuana consumption, 2. obtain a medical marijuana ID card from his state health department (to be eligible to shop at MMJ dispensaries), 3. find a dispensary which sells RSO. Some states have home delivery or ship their products. Good luck.

      • enubus

        Thanks for your concern,, but I doubt he would consider that.

        • Yvonne Forsman

          I understand. You can lead a horse to water but you can’t make it to drink. I have a friend in California where medical cannabis is legal. She was diagnosed with cancer and I told her to get the cannabis but she went along with her doc suggestion of chemo. She also had a biopsy which led to spreading of the cancer throughout her body. She stopped the chemo now b/c she realized it doesn’t help, it only destroys her immune system. So thanks to her medical doctor she now has cancer in her whole body. Sad. But I also happened to watch a video where somebody mentioned her sister has a cancer and I managed to find her email address thru google and told her the sister’s life can be saved by cannabis. To my surprise she responded to my email, saying her sis lives in California and has used the Rick Simpson oil and has healed the original tumor, now successfully battling metastases. I was very happy to hear that. Every life is worth saving!

    • Ruth Griffith

      detox his body build his immune and juice with dark green veggies , he needs to do colon cleaning to keep bad bacteria from getting into his body

      • enubus

        okay, thanks

  • paleobird

    I had horrendous IBS-like symptoms for about a year post chemo until I went paleo and cut out the gluten. I had never had problems with it before.

    • Ruth Griffith

      colon clean with organic coffee or tumeric


    As you and others have repeated, chemo and antibiotics, as you stress, are sometimes essential. I am at the beginning of long term treatment of antibiotics for bronchiectasis with MAC. What can I do (or take) to counter the ravage of the unavoidable multi antibiotics to repair,replace, maintain, good microbioms?? RSVP. Thank you Dr. Perlmutter

    • Ruth Griffith

      you can eat garlic or take apple cider vingar both are antibotics , also use distilled water baking soda and lemon in the mornings and at night

  • Denise Menagh

    So do you HAVE to have a fecal transplant to repopulate the gut after chemo? Or could you just eat a bunch of probiotics, yogurt & apple cider vinegar? 😉 I smile bc I feel like I know what your answer is going to be, and I guess in the case of a patient taking chemo for say, breast cancer, it is a lifesaving treatment, but would insurance even cover a fecal transplant for this?

    • David Perlmutter

      Unfortunately, insurance would not cover this as it is not a currently approved treatment by the FDA.

      • Denise Menagh

        What I meant to say (besides the insurance question) is, is FMT the ONLY way to repopulate the microbiome after chemotherapy, or are there other, less invasive, ways to accomplish that?

        • Ruth Griffith

          you need to detox your body after chemo and take immune booster

    • Yvonne Forsman

      I had chemo 16 years ago, did not understand the importance of good/balanced microbiome until very recently, so now I am trying Colostrum (see link). 2 yrs ago I also stopped all grains and started org kefir and sauerkraut. My health has deteriorated ever since the chemo. Thanks God for Dr Perlmutter and Dr O’Bryan!

      • Ruth Griffith

        also eat veggies , juice and get the proper vitamins , minerals are a must some herbs would be great for you also

    • maria

      Denise, as no one else is answering your question, I’ll try my hand at it. I think eating a lot of fermented food and taking supplements would be a big step in the right direction. I’ve read (in the New Yorker, I think) about people self-administering fecal transplants, but it you are very ill, you should research further. This is a new field, with main stream medicine lagging behind.

      • Denise Menagh

        And… that’s crazy… self-administering a FMT… :/

  • Leonie Gittins

    I believe my ‘IBS’ started with the chemo I was given for Ovarian cancer 25 years ago. I had cyclophosphamide and cisplatnin (sorry, not sure of the correct spelling). It gradually worsened until I cut out out wheat, onions and garlic (FODMAPS). Leonie in Australia

  • Brenda

    I am on a weekly chemo agent (methotrexate) for severe colitis. When I was very ill and hospitalized 4 yrs ago during a severe flare up one doctor suggested I take a specific probiotic for people with crohns & colitis (it’s called VSL #3) What a HUGE difference it made in my health !!!! It’s contains 450 billion live cultures. Wouldn’t be without it!

    • Ruth Griffith

      all people should do probotics and eat veggies and juice how is your bowels now . do u do a colon cleaning to keep bacteria out of your bowels at least every 3 months. it is good if u do because, it can keep the bacteria from getting into your stomach and rest of your body , also u need to detox your body after chemo because it helps rid your body from toxins that the chemo put in you

  • Very fascinating, thanks for sharing!

  • Mary Anne Polovich Griffin

    Dr. Perlmutter, thank you for your timeliness on this article and any advice you might be able to give me. I’m due to start chemo for breast cancer in 10 days, and I’m wondering if you have recommendations for anything I can possibly do in this short of time to prepare my gut?

    • Sean Tracey

      If you dont mind me saying there is a wealth of information available on alternative (natural) cancer therapies. Believe it or not things such as carrot juice, bi carb soda (baking soda) beetroot juice and tumeric have been known to cure of assist with curing cancer. There is actual science behind these things. You could look up facebook “Chris beat cancer” or “Essiac Tea” , both pages have a wealth of information. All of these things can be done with Chemo but hopefully will shorten the duration of your treatment.

      Wishing you the best of luck.

      • Ruth Griffith

        that is right

    • Ruth Griffith

      do a detox with black wallnut hull then get an immune support make sure you eat veggies , juice and do milkthistle

  • Ruth Griffith

    if you have cancer of any kind you should never eat sugar , nor should you do red meat , also as for chemo it has been proven that it does cause more canceer in the cancer patient. a cancer patient should juice , do minerals , and vitamins , boost their immune , keep their colon clean , detox their bodies from parsites and bacteria with black wallnut hull , flax seed and grape seed are great for the cancer patient ,. dandlion root is like a chemo treatment . enchinea is like a chemo trearment . aprocot seeds are great for the cancer patient . stay away ffrom white breads , bleached flour meaning any white flour , also milkthistle should be taken it helps your liver and it protects your liver . lemon,and baking soda and distilled water is great for the cancer patient. to the people who have breast cancer try not to ware a bra because it stops the natural flow of the blood in your breast , they are right now doing studies on the bra and the breast .reshi or matike mushrooms are great for the cancer patient
    hyper therma is good for the cancer patient . ferminted foods are good for the cancer patient

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