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5 Steps to Kill Hidden Bad Bugs in Your Gut that Make You Sick

5 Steps to Kill Hidden Bad Bugs in Your Gut that Make You Sick

DOCTORS ARE TRAINED TO IDENTIFY DISEASES by where they are located. If you have asthma, it’s considered a lung problem; if you have rheumatoid arthritis, it must be a joint problem; if you have acne, doctors see it as a skin problem; if you are overweight, you must have a metabolism problem; if you have allergies, immune imbalance is blamed. Doctors who understand health this way are both right and wrong. Sometimes the causes of your symptoms do have some relationship to their location, but that’s far from the whole story.

As we come to understand disease in the 21st century, our old ways of defining illness based on symptoms is not very useful. Instead, by understanding the origins of disease and the way in which the body operates as one, whole, integrated ecosystem, we now know that symptoms appearing in one area of the body may be caused by imbalances in an entirely different system.

If your skin is bad or you have allergies, can’t seem to lose weight, suffer from an autoimmune disease or allergies, struggle with fibromyalgia, or have recurring headaches, the real reason may be that your gut is unhealthy. This may be true even if you have NEVER had any digestive complaints.

There are many other possible imbalances in your body’s operating system that may drive illness, as well. These include problems with hormones, immune function, detoxification, energy production, and more. But for now, let’s take a deeper look at the gut and why it may be at the root of your chronic symptoms.

Symptoms Throughout the Body Are Resolved By Treating the Gut

Many today do have digestive problems including reflux or heartburn, irritable bowel, bloating, constipation, diarrhea, and colitis. In fact, belly problems account for over 200 million doctor’s visits and billions in health care costs annually. But gut problems cause disease far beyond the gut. In medical school, I learned that patients with colitis could also have inflamed joints and eyes and that patients with liver failure could be cured of delirium by taking antibiotics that killed the toxin-producing bacteria in their gut. Could it be that when things are not quite right down below, it affects the health of our entire body and many diseases we haven’t linked before to imbalances in the digestive system?

The answer is a resounding yes. Normalizing gut function is one of the most important things I do for patients, and it’s so simple. The “side effects” of treating the gut are quite extraordinary. My patients find relief from allergies, acne, arthritis, headaches, autoimmune disease, depression, attention deficit, and more—often after years or decades of suffering. Here are a few examples of the results I have achieved by addressing imbalances in the function and flora of the gut:

  • A 58-year-old woman with many years of worsening allergies, asthma, and sinusitis who was on frequent antibiotics and didn’t respond to any of the usual therapies was cured by eliminating a worm she harbored in her gut called Strongyloides.
  • A 52-year-old woman who suffered with daily headaches and frequent migraines for years, found relief by clearing out the overgrowth of bad bugs in her small intestine with a new non-absorbed antibiotic called Xifaxin.
  • A six-year-old girl with severe behavioral problems including violence, disruptive behavior in school, and depression was treated for bacterial yeast overgrowth, and in less than 10 days, her behavioral issues and depression were resolved.
  • A three-year-old boy with autism started talking after treating a parasite called Giardia in his gut.

These are not miracle cures but common results that occur when you normalize gut function and flora through improved diet, increased fiber intake, daily probiotic supplementation, enzyme therapy, the use of nutrients that repair the gut lining, and the direct treatment of bad bugs in the gut with herbs or medication.

A number of recent studies have made all these seemingly strange reversals in symptoms understandable. Let’s review them.

Research Linking Gut Flora and Inflammation To Chronic Illness

Scientists compared gut flora or bacteria from children in Florence, Italy who ate a diet high in meat, fat, and sugar to children from a West African village in Burkina Faso who ate beans, whole grains, vegetables, and nuts.(i) The bugs in the guts of the African children were healthier, more diverse, better at regulating inflammation and infection, and better at extracting energy from fiber. The bugs in the guts of the Italian children produced by-products that create inflammation, promote allergy, asthma, autoimmunity, and lead to obesity.

Why is this important?

In the West, our increased use of vaccinations and antibiotics and enhancements in hygiene have lead to health improvements for many. Yet these same factors have dramatically changed the ecosystem of bugs in our gut, and this has a broad impact on health that is still largely unrecognized.

There are trillions of bacteria in your gut, and they collectively contain at least 100 times as many genes as you do. The bacterial DNA in your gut outnumbers your own DNA by a very large margin. This bacterial DNA controls immune function, regulates digestion and intestinal function, protects against infections, and even produces vitamins and nutrients.

Can bacteria in the gut actually affect the brain? They can. Toxins, metabolic by-products, and inflammatory molecules produced by these unfriendly bacteria can all adversely impact the brain.

When the balance of bacteria in your gut is optimal, this DNA works for you to great effect. For example, some good bacteria produce short chain fatty acids. These healthy fats reduce inflammation and modulate your immune system. Bad bugs, on the other hand, produce fats that promote allergy and asthma, eczema, and inflammation throughout your body.(ii)

Another recent study found that the bacterial fingerprint of gut flora of autistic children differs dramatically from healthy children.(iii) Simply by looking at the by-products of their intestinal bacteria (which are excreted in the urine—a test I do regularly in my practice called organic acids testing), researchers could distinguish between autistic and normal children.

Think about this: problems with gut flora are linked to autism. Can bacteria in the gut actually affect the brain? They can. Toxins, metabolic by-products, and inflammatory molecules produced by these unfriendly bacteria can all adversely impact the brain. I explore the links between gut function and brain function in much greater detail in my book, The UltraMind Solution.

Autoimmune diseases are also linked to changes in gut flora. A recent study showed that children who use antibiotics for acne may alter normal flora, and this, in turn, can trigger changes that lead to autoimmune disease such as inflammatory bowel disease or colitis.(iv)

The connections between gut flora and system-wide health don’t stop there. A recent study in the New England Journal of Medicine found that you could cure or prevent delirium and brain fog in patients with liver failure by giving them an antibiotic called Xifaxan to clear out bugs that produce toxins their poor livers couldn’t detoxify.(v) Toxins from bacteria were making them insane and foggy. Remove the bacteria that produce the toxins, and their symptoms clear up practically overnight.

Other similar studies have found that clearing out overgrowth of bad bugs with a non-absorbed antibiotic can be an effective treatment for restless leg syndrome(vi) and fibromyalgia.(vii)

Even obesity has been linked to changes in our gut ecosystem that are the result of a high-fat, processed, inflammatory diet. Bad bugs produce toxins called lipopolysaccardies (LPS) that trigger inflammation and insulin resistance or pre-diabetes and thus promote weight gain.(viii)

It seems remarkable, but the little critters living inside of you have been linked to everything from autism to obesity, from allergy to autoimmunity, from fibromyalgia to restless leg syndrome, from delirium to eczema to asthma. In fact, the links between chronic illness and gut bacteria keep growing every day.

So what can you do to keep your gut flora balanced and your gut healthy, and thus overcome or avoid these health problems?

Five Steps to a Healthy Gut (and a Healthy Body)

Follow these five simple steps to begin re-balancing your gut flora:

  1. Eat a fiber–rich, whole foods diet—it should be rich in beans, nuts, seeds, whole grains, fruits, and vegetables, all of which feed good bugs.
  2. Limit sugar, processed foods, animal fats, and animal protein—these provide food for unhealthy bugs.
  3. Avoid the use of antibiotics, acid blockers, and anti-inflammatories—they change gut flora for the worse.
  4. Take probiotics daily—these healthy, friendly flora can improve your digestive health and reduce inflammation and allergy.
  5. Consider specialized testing—such as organic acid testing, stool testing (new tests can look at the DNA of the bacteria in your gut), and others to help assess your gut function. You will likely have to work with a functional medicine practitioner to effectively test and treat imbalances in your gut.

And if you have a chronic illness, even if you don’t have digestive symptoms, you might want to consider what is living inside your gut. Tending to the garden within can be the answer to many seemingly unrelated health problems.

Please leave your thoughts by adding a comment below—but remember, we can’t offer personal medical advice online, so be sure to limit your comments to those about taking back our health!

To your good health,
Mark Hyman, MD


(i) De Filippo, C., Cavalieri, D., Di Paola, M., et al. 2010. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA. 107(33): 14691–6

(ii) Sandin, A., Bråbäck, L., Norin, E., and B. Björkstén. 2009. Faecal short chain fatty acid pattern and allergy in early childhood. Acta Paediatr. 98(5): 823–7.

(iii) Yap, I.K., Angley, M., Veselkov, K.A., et al. 2010. Urinary metabolic phenotyping differentiates children with autism from their unaffected siblings and age-matched controls. J Proteome Res. 9(6): 2996–3004.

(iv) Margolis, D.J., Fanelli, M., Hoffstad, O., and J.D. Lewis. 2010. Potential association between the oral tetracycline class of antimicrobials used to treat acne and inflammatory bowel disease. Am J Gastroenterol. Aug 10 epub in advance of publication.

(v) Bass, N.M., Mullen, K.D., Sanyal, A., et al. 2010. Rifaximin treatment in hepatic encephalopathy. N Engl J Med. 362(12): 1071–81.

(vi) Weinstock, L.B., Fern, S.E., and S.P. Duntley. 2008. Restless legs syndrome in patients with irritable bowel syndrome: response to small intestinal bacterial overgrowth therapy. Dig Dis Sci. 53(5): 1252–6.

(vii) Pimentel, M., Wallace, D., Hallegua, D., et al. 2004. A link between irritable bowel syndrome and fibromyalgia may be related to findings on lactulose breath testing. Ann Rheum Dis. 63(4): 450–2.

(viii) Cani, P.D., Amar, J., Iglesias, M.A., et al. 2007. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes. 56(7): 1761–72.

Mark Hyman MD is the Medical Director at Cleveland Clinic’s Center for Functional Medicine, the Founder of The UltraWellness Center, and a ten-time #1 New York Times Bestselling author.

Comments (89)

  • I have been told I have leaky gut. I would love to know what supplements to heal it. But, no matter what dairy free, etc.probiotic I take I react. Pain, severe bloating, headache, muscle pain and joint pain. Any mix of the above. Suggestions?

    • You might want to try these two Tao Free Samento and SerraEnzyme. Both are anti-inflamatories. Boost immune system. Lower blood pressure. and help with intestinal issues, back pain caused by inflammation, muscle Spasms….

    • Joanna,
      One of the main causes of leaky gut is gluten. The Doctor who diagnosed you should do a blood test for your Ttg levels. At age 61 I was finally diagnosed with Celiac disease after having leaky gut for 3 years, and loss of muscle in my legs. It took tow years of going gluten-free to heal my gut, and I began to despair after the first year. So if you are already gluten-free and not better, you may need to go grain free too until you heal – on something like the Specific Carbohydrate diet, which uses nut flours for your bread and baking. Instead of dairy yogurt, you can use coconut yogurt and vary your probiotics to get a wide range of them into your gut.
      The main message is that a supplement will not heal your gut as much as a very strict gluten-free diet and to digest your food better until you heal, you can use pancreatic enzymes, as the pancreas us usually compromised as well. Dr. Hyman has mentioned this in his books.

      • Please fix my typing mistakes in the above message, as I don’t see a place to edit my message.

    • I know this is almost a year old, but you’re looking for L-Glutamine powder. Take between 20-40 grams per day, avoid high gluten foods, and enjoy the healing.

      • I’m confused the Dr is talking favorably about using an anti biotic they are what got me in trouble in the first place very confused

    • Hello,

      I understand you asked this a long time ago, I hope you found a solution. However for anyone else reading or yourself.

      LEAKY GUT: Take L-Glutamine powered form. Mixed with water.
      L-Glutamine is an important amino acid that all cells require to function. Naturally it is stored in the lungs it is released slowly.
      However another benefit of L-Glutamine is that it is very good at healing sores and cells in the gut.
      Taking this as a supplement with heal up a leaky gut within days-weeks.
      Fortunately L-Glutamine is taken by the body building society for other benefits related to muscle repair so it is easily available and cheap. I would recommend this website:

      I hope this helps at least one person.

      Eddie Rourke.
      Crohns Disease. (Really helped this too.)

    • You need the GAPS book to learn how to heal leaky gut. Supplements alone cannot do it. It’s called Gut and Psychology Syndrome by Dr Natasha Campbell-McBride.

  • I am confused. You say to limit animal fat and protein but your diet is not vegetarian. In fact, I have been eating more animal protein since on your diet. can you please explain?

    • Hi Stephanie, my understanding is that nutrition is complex, there are few hard and fast rules. I think Hyman is saying that in general, less animal fat and protein is less inflammatory. I think he’s speaking to the usual S.A.D. (standard american diet) that is very high in poor quality meat, refined grains, sugar…etc. Less meat in that context may be better. (and higher quality meat, and perhaps entirely less *red* meat!) But we do need protein, for many reasons. So we do need to eat some protein. And moderate quality animal protein *is* good for us for many reasons. Many people will even not do well on a vegan diet…I have read several times about people who’s health improved when they finally added meat back into their diet. So try not to think of it as black and white. When you go deeper into it (deeper than just one article giving general advice) you see that in depends on the individual, and everything works together. The 10 Day Detox as I understand, is a Total Package. I think we can trust it…Dr.Hyman knows if anyone does!

      • The best advice/program is always individual, with thorough testing, etc. But Hyman can’t be everywhere. And Functional Medicine practitioners are still relatively few (I think, I could be wrong!) Hyman writes books, creates programs…to help more people….I think he’s doing a brilliant job!

    • I was also thrown by the condemnation of animal fats and protein. They do not feed bad bacteria.   Protein, and especially fat, from organic, pastured, appropriately fed animals are the cornerstone of the GAPS diet, which is the only protocol I know of that heals and seals the gut lining. Also, the promotion of whole grains and starches like beans, which overwhelmingly *do* feed the pathogens. With all due respect, I believe this article is misinformed.

  • I have a co worker who’s husband has Crohn’s disease and I guess is on the normal regimen. He is mid 30’s. What test’s would you recommend other than what you have mentioned and, have you ever seen anyone able to reverse this? I did recommend to her that he take digestive enzymes and probiotics, and protyoletic enzymes.

    • We have a cousin diagnosed with Crohn’s who was prescribed a $2000/mo drug that made him feel like his heart was going to explode. He quit taking it and started Phillips Probiotics. He now has good days and bad days.

    • Crohn’s is often gluten intolerance – try gluten free. Cows milk products are also inflammatory. Omega 3 is anti-inflammatory – wild fish oil for men, flax oil for women (we find 4/day is good – 2 + 2). Health food store brands only, like Spectrum or Barleans.. Best probiotic we’ve found is REAL sauerkraut – (unpasteurised) – not easy to find but Bubbies seems to be widely available.

      • Crohn is NOT gluten intolerance. Celiac is the gluten intolerance. Crohns is a whole different issue.

  • Kefir with Goat Milk is the best thing I’ve ever done and I’ve taken many expensive probiotics. Go buy some Kefir grains locally on Craigslist. (Don’t use water kefir (tibicos). It’s not effective for repopulating the colon.) Your ancestors all relied on Kefir for a hearty immune system.

    • Thanks for the suggestion, Jeff 🙂 Sad to say I have tried Kefir as well before I found out I can’t tolerate lactose. Huge headache and muscle/joint pain. Once I figured the dairy. issue, I switched to dairy free brands. Still no luck. Stinks.

      • Johanna, Try kefir or regular yoghurt cultures, but give them more time. If you use regular yoghurt culture but “incubate” them for 24hrs @ 100 degrees almost all of the lactose will be gone – eaten by the cultures!

      • There is a dairy free probiotic drink made from young green coconuts called Inner Eco. It is sold in the whole body department of most Whole Foods and is (in my opinion) one of the best probiotic beverages on the market.

    • I agree with that but I can’t find milk that allows the grains to grow. When I had raw goat milk, it worked great but goat milk is not common.

  • Excellent article with so much valuable advice! I see so many chronically ill people and their diets are horrible. Thank you for keeping us informed!

  • I’ve been working with an Integrative Dr. and have one last test to do before my follow-up. You guessed it – stool test. However I’ve been told that it is not as complete compared to taking a stool sample to a local vet for testing – as they are more thorough and can detect worms, bugs, etc.
    Any information on this would be appreciated….

    • Go to the net and find Smokey Mountain Diagnostics. This is a lab that does stool cultures. They do a very thorough job of detailing in a multipage report all their findings. You must go through your doctor, and they will be sent the report for a complete interpretation.

  • I am curious how long this “new” antibiotic has been on the market? How many studies on the long term effects of it have been done and what those show. I took tetracycline for years for acne and it seemed to be addressing the issue of acne but the LONG TERM effect was obviously that my intestinal microbiota had been alter…and not in a good way. I have concern for the use of the “new non-absorbed antibiotic” mentioned in this article!

  • Your article offers great suggestions such as avoiding all processed foods and taking daily probiotics. However, it only briefly mentioned yeast overgrowth which is a major problem in America. Yeast is a fungus that lives in everyone’s gut. Good bacteria keeps it in check, but if it gets t upper hand, it causes all sorts of havoc in the body. Until I started taking antifungals like Olive Leaf Extract and following the Phase One diet a recommended by Doug Kaufman on his show “Know the Cause” I could not get resolution to my health problems which included IBS and migraines.

  • An allergy/environmental doc prescribed me SF722 (10-Undecenoic Acid) for candida/toxic mold exposure, along with probiotics. Recently the SF722 was unavailable for nearly a year due to a governmental agency taking it off the market–I am not sure exactly why… I believe that was one of the factors leading to multiple ER visits and a series of serious infections for me. (The other major factor being difficulty in getting my formulary prescription of potent antioxidants filled.) As a last resort I took “real” antibiotics–it took three rounds of them, along with prednisone, to begin healing. (I tried many natural antibiotics first, but after loosing hearing in one ear, I was pretty desperate.) And I am still using garlic, with allicin,– just started l-lysine, also gargling with hydrogen peroxide and water–had to stop gargling with mouthwash due to feet/leg swelling– taking liquid chlorophyll in water, organic green juice daily, charcoal and bentonite clay taken at prescribed intervals, chicken broth made with crushed garlic, coconut oil, oregano oil, sea salt & lemon juice–and at various times: colloidal silver, zinc, an immune system effervescent tablet in water, & sublingual cold/flu tablets.
    My system has strong, rapid, negative response to sugar in any form. During the time of infection, I ate a small amount of quality protein, my organic green juice and a few raw veggies–& very rarely a few dark berries. If I had any sugar, even a half teaspoon raw honey in my tea, the infection would rage, (along with a laundry list of other negative sx).Tripling my krill oil, no longer gives the cognitive improvement I’d previously enjoyed. I agree that functional medicine is key, in treating chronic illness–especially illness related to our increasingly toxic environment.

  • thankyou for the advise,very helpful,living a healthy life hence healthy brain,body.balance life with no un-necessary hussle from ???????????????????????????????????????????

  • Excellent article. Thank you! I have been wanting to start my family on probiotics, but I am overwhelmed with the various probiotics available. How do I decide which to buy? Is a pill the way to go or kefir or growing own water kefir? I have a lot to learn! And what about probiotics for children–how do I know what will be best for them? And what about my baby that hasn’t started solids, but has eczema–I am assuming probiotics in my diet will help her, but again–unclear on where to start.

  • Thank you for this excellent article. One of the best I have read on this topic! You’re doing a great service to so many by sharing your expertise and insights on natural health and functional medicine!

  • I have been diagnosed with a fibroid, which is still about 1,2cm, my research about fibroid tumors acquired information relating to hormonal imbalances. I have since adopted a strict vegan diet. I do see changes in my body but I still have irregular waste excretion. How can Improve this using diet. I have tried colon detoxing using psyllium husk but its not as effective. What can l do to help the situation.

    • Thank you for your interest in Dr Hyman’s work. Unfortunately Dr Hyman cannot provide personal medical advice in this forum. For more personalized nutrition advice, Dr Hyman’s nutrition coaching team would be happy to work with you on an individual level to help you reach your goals. To work with the nutrition coaching team please go to: OR call (800) 892-1443 to get started.

    • If you have a fibroid and its due to hormonal imbalances, do not eat soy in your strict vegan diet. That’s what causes my fibroid. Soy has a plant estrogen that can and does affect the body in different ways, usually in hormonal ways.

  • After suffering from IBS for 3 months plus and losing 25 Lbs(6 foot weighing 140). I read this information about xifaxan and went to PCP who gladly prescribed. Went to health food store and got a good fiber supplement and awaiting prescription of VSL #3..Well 5 days no bouts of running to toilet..Feel better and have more energy….My Gastro gave me anti spasmatics for the RUNS..nothing else…If I didn’t look up this info I would still be suffering…..Your GUT runs your body! My favorite high Fiber food is raspberries ……..So far so good….The advice offered on this site has changed my life…There is hope

  • My mum is dying from recurring abdominal sepsis, we’re trying probiotics. Shes had round after round of antibiotics both IV and tablet form. Can anything natural help her? We are thinking of Hydrogen Peroxide.

    • Thank you for your interest In Dr. Hyman’s work. Unfortunately he cannot provide you personalized medical advice in this forum. In order to provide you the proper care you need we hope you will seek the attention of a local qualified Functional Med practitioner soon. To locate a doctor near you who practices functional medicine like Dr. Hyman, go to and scroll down to where it says “locate a practitioner” and enter your location. Progress accordingly from there.
      You can also make an appointment to be a patient at Dr.Hyman’s UltraWellness Center in Lenox, MA. Please go to:
      Did you know you can work with Dr. Hyman’s nutritionists virtually? For personalized nutrition coaching, please see:
      In Good Health,
      Dr. Hyman’s Wellness Staff

    • Pls investigate Young Living essential oils. Read about the internal cleansing.
      Purification and implants. Saving my life.

  • I like reading these kind of articles. I have always absorbed whole foods ideas since being a teenager and am 51 now. Only used a Doctor 2 or three times in that time. These 5 steps — they make sense, most doctors do not think this way. I could use more information on how to talk to Doctors, to get what is needed and get them to agree

    What does it mean to, ” Limit sugar, processed foods, animal fats, and animal protein—these provide food for unhealthy bugs? ” It is hard to take action on Limit. I am not sure what limit means here. This is an extreme variable at best.

    In addition, nothing is said about fasting and it affects bugs. And if one fasted, how would they do it. I need a real fasting Doctor, I have fasted in extreme ways. I have found Doctors are not knowledgeable about fasting, my experience fasting, teaches me things, Doctors do not know. Perhaps they themselves have not done this or studied much about it.

    I juice a lot with fruits and vegetables —- I do not get hungry for fiber–rich, whole foods. I do get hungry for sugar from time to time. Not sure what is going on with me. I do not eat processed foods as a rule or huge amounts of meat, but sometimes I get hungry for meat and have felt weak, till I ate a good steak, then my strength came back. I seldom ever feel weak while fasting even up to 66 days. I want to fast more….because it feels so good. However, all the medical data I read seems to indicate extreme ignorance on this subject.

    Would appreciate any info you can direct me towards!!!! Thanks —- Doctor.

    • Hi Rick,
      Thank you for your interest In Dr. Hyman’s work. Unfortunately he cannot provide you personalized medical advice in this forum. In order to provide you the proper care you need we hope you will seek the attention of a local qualified Functional Med practitioner soon. To locate a doctor near you who practices functional medicine like Dr. Hyman, go to and scroll down to where it says “locate a practitioner” and enter your location. Progress accordingly from there.

      You can also make an appointment to be a patient at Dr.Hyman’s UltraWellness Center in Lenox, MA. Please go to:

      Did you know you can work with Dr. Hyman’s nutritionists virtually? For personalized nutrition coaching where you can receive 1:1 support with Registered Dietitians, please see:
      Wishing you the best of health,
      Dr. Hyman Staff

  • Excellent Article. Bad parasites creates all this mess. Thanks to Dr. Hyman’s for sharing this info. Finding the root case is one important factor in Medication but modern medical treatment misses this or wrong diagnostic approach that gives wrong results. Correct root cause analysis and proper selection of medication solves any critical health issue with ease.

    Information available across the world and solution can be achieved only through spreading the right info at right time thro right people.

    Let’s go with the natural approach with natural resources…..

    Be health and be happy !!!!!

    Mr. U

  • Dr. Hyman, I am curious as to your thoughts on grains, beans, nuts and seeds, and their enzyme inhibitor, and/or lectins, and/or phytic acid content, and how those anti-nutrients impact digestion and nutrient availability and absorption.

    I have read a lot of papers from Chris Kresser L.Ac., and while he isn’t an MD, he has done a LOT of nutritional research, and he feels that some animal protein and fats are healthy for the body.

    So my question it this: when will your work and his work (or others like him, e.g. those in the traditional foods community) MERGE and find the common ground that is so sorely needed in nutritional medicine today?

    Thank you, Dave

  • Ibs with constipation and sharp pain in left side my two sisters have also been having ibs issues..not sure what they are doing to get better….im Finally feeling a little better after doing maralax for four months. Doctor prescribe ..And also i am having a dull pain in my right side now so the pain is now in both sides but not near as bad as it was….. This all started over three years ago when i got really sick and could not breathe after meals! Left pain was bad… Leaking gut too..They told me it was asthma after ordering a damned expensive heart cath scan…… So now i have fiqured out the gut issues have caused my asthma because after regular bowl movements no more asthma! Also Prevacid helps me not get asthma and seems to help me feel better too… I cant help but think im in a battle with some type of bad bacterial infection. Eating an apple every morning helps too.. So for the first time in years no leaking gut.. My bowls are empty all the way… But I’m still not normal because without maralax and Prevacid and an apple I’m back feeling sick…

    I have good insurance .. And i live in Nashville .. Do you know a good intestinal health doc ?? Close to me??? I feel 1000 times better than 3 years ago but need a doctor to get my intestines right right.

  • I have been in a Paleo diet since November of last year. I eat bacon and eggs every single morning with a kiwi fruit in the morning and afternoon. I have Tuna,steak, with Paleo coconut wrap with almond butter every day at lunch time, then at dinner I have salad and meat,fish,pork,poultry. All my meat is grass fed to include eggs,bacon. All my veggies, nuts, are organics and I exercise 5 days a week. I find that this, after being told that I had emphysema, is an amazing progress from then. I have no symptoms and my lungs are extremely good since I became exercise incline. It’s my understanding that exercising is a must for a healthy body. Last but not least, I do take probiotics, omega 3, ubiquinol, alfalfa tables, and cordyceps. My life has change because I believe my gut flora have become balance by my efforts.

  • Given that there are so many probiotics being marketed, how does one go about making a selection? There are too many options for various health products, it’s hard to know which ones are reputable and which ones aren’t. I’m always skeptical about companies that make claims accompanied by a high price tage.

    Thank you, Miss L.

    • Hi Louise,

      There’s lots of information out there and it can be confusing! We recommend Ther-Biotic Complete capsules made by Klaire/Prothera. They can be found in the wellness store or they can be found online and other retailers.

  • This is a really interesting topic. It’s amazing how the gut can really effect all different parts of the body. Natural solutions seem a lot more beneficial. Thank you.

  • I am a 49 year old woman who was born with diarrhea. I am being treated for ibs, am lactose intolerant, have diabetes, fatty liver disease, high blood pressure, depression and a nervous stomach. I’ve had 4 children and had gestational diabetes with all 4 only treated for it with my last child. My children all weighed more than 9 lbs. with an 11 lb. baby being my biggest. It took a year for my blood sugar to get under control no insulin anymore just 2 pills a day. I need someones help, need to lose weight, exercise, and feel better. Thanks, Diana

    • Hi Diana,
      Thank you for your interest In Dr. Hyman’s work. Unfortunately he cannot provide you personalized medical advice in this forum. In order to provide you the proper care you need we hope you will seek the attention of a local qualified Functional Med practitioner soon. To locate a doctor near you who practices functional medicine like Dr. Hyman, go to and scroll down to where it says “locate a practitioner” and enter your location. Progress accordingly from there.

      You can also make an appointment to be a patient at Dr.Hyman’s UltraWellness Center in Lenox, MA. Please go to:
      Wishing you the best of health,
      Dr. Hyman Staff

    • Hi Brenda,
      There are many good probiotic supplements available on the market, and we recommend that your work with your doctor to determine the appropriate bacterial strains to balance your digestive tract. If you would like to review the brands that Dr. Hyman recommends to his patients, please see
      Wishing you the best of health,
      Dr. Hyman Staff

  • Good day I am a Colon Hydrotherapist in Windhoek, Namibia and would like to hear what your opinion is about this therapy. I noticed good results in myself and many of my clients i.c.w. more energy, no more cravings, weight loss, improvement of sinusitis after cleansing their bowels and treating with probiotocs and a healthy diets (lots of veggie juices etc.) The Doctors here do not support this therapy. Would appreciate if you could give me your opinion. Thank you

  • Hi Dr.,

    I suffer from IBS which seems like a bacterial overgrowth that began after I drastically increased the amount of fruits and starches in my diet, and limited or completely removed sources of animal protein and fats. I am trying to heal myself now, and the only foods that don’t seem to cause bloating, gas and acne are meats, along with nuts, seeds, and small amounts of bread and very limited amounts of fruit (and only specific kinds). Above, you mention that animal fats can feed the bad bacteria, however I have been eating a lot of it lately. Is this not a good idea? What would you advise? It doesn’t seem to bother my digestion now; its all I can eat! My diet was previously nearly completely plant-based and what most would consider “healthy”, but it completely backfired on me and destroyed my gut health. I can’t even drink coffee anymore without bloating and discomfort. I am at a loss for what to do. I began taking caprylic acid recently which helped with the itchiness
    ‘down there’. What should i be looking toward for a cure? Thanks

    • Hi Isabella,
      Thank you for your interest In Dr. Hyman’s work. Unfortunately he cannot provide you personalized medical advice in this forum. In order to provide you the proper care you need we hope you will seek the attention of a local qualified Functional Med practitioner soon. To locate a doctor near you who practices functional medicine like Dr. Hyman, go to and scroll down to where it says “locate a practitioner” and enter your location. Progress accordingly from there.
      Wishing you the best of health,
      Dr. Hyman Staff

    • I know this was posted a while ago…but have you considered fructose/sucrose intolerance? I am fine with meats too, fruit/sugar upsets me and now I’m considering this explanation myself. Good luck.

  • So it started with me 7 years ago. My stool changed. It’s not properly digested, it’s always green or orange. Always floats. When I say all these symptoms to my gastrologist he tells me stool doesn’t have to sink and the color varies. I don’t find his answer satisfying.
    I’m commenting to this article, because I found lots of similarities to what dr. Hyman says. When my stool changed, short after that, I started having constant and persistent acid reflux (never had that problem before). Then my eye sight changed. I noticed that sometimes when I read, it’s little blurry. Went to ophthalmologist and he told me my eye sight was normal. I have far more symptoms then that, but it’ll take me forever to list them here.
    I just want to know if there’s any help to end my suffering.

    • Hi Marie,
      Thank you for your interest In Dr. Hyman’s work. Unfortunately he cannot provide you personalized medical advice in this forum. In order to provide you the proper care you need we hope you will seek the attention of a local qualified Functional Med practitioner soon. To locate a doctor near you who practices functional medicine like Dr. Hyman, go to and scroll down to where it says “locate a practitioner” and enter your location. Progress accordingly from there.

      You can also make an appointment to be a patient at Dr.Hyman’s UltraWellness Center in Lenox, MA. Please go to:
      Wishing you the best of health,
      Dr. Hyman Staff

  • Dr. Hyman,

    Thanks for this useful article. I am suffering from stomach/gut pain in the left side of my body for the last 6 months. I have lost weight in the process. There is also a lot of gas. Initially the doctor gave a lot of pills. They gave some relief but did not bring about a permanent cure. I suspect it all started with some adulterated/stale milk that I drank outside.

    Now I have stopped seeing any doctor. I take probiotic Yakult drink daily after lunch. Sometimes I take Danone yogurt at night. These are giving good relief. No more pills. However, whenever I eat spicy food or eat a large meal, I have trouble. I would like some suggestions on a permanent cure. I am not looking for a quick cure. Even if it takes a few months, I am okay with that. Are there certain foods that I can take to cure this problem in a natural way?

    Thank you.

    • Thank you for your interest In Dr. Hyman’s work. Unfortunately he cannot provide you personalized medical advice in this forum. In order to provide you the proper care you need we hope you will seek the attention of a local qualified Functional Med practitioner soon. To locate a doctor near you who practices functional medicine like Dr. Hyman, go to and scroll down to where it says “locate a practitioner” and enter your location. Progress accordingly from there.
      Wishing you the best of health,
      Dr. Hyman Staff

  • Hi… Soybeans contain 35–40% protein on a dry-weight basis, of which 90% is comprised of 2 storage globulins, 11S glycinin and 7S β-conglycinin (10). Glycinin has A (acidic) and B (basic) subunits, whereas β-conglycinin has α, α′, and β subunits. These proteins contain all amino acids essential to human nutrition, which makes soy products almost equivalent to animal sources in protein quality but with less saturated fat and no cholesterol…. my question is that is it still harmful to gut???

  • Get tested for Prevotella copri, folks.

    This seems to be one of the key gut microbes causing many autoimmune disorders (leaky gut, celiac, roseacea, chronic headaches, seasonal allergies, food allergies, etc). All of them can often be linked to the body attacking food and digestive particles getting in from the intestines because of damage caused by bacteria.

    Not unlike how H.pylori was linked to chronic heartburn in recent years.

    Healthier diets with probiotics, limited sugars, and starches DO help in promoting good bacteria growth, that combat the bad bacteria. However, some of us will need some medical help to get rid of the bad bacteria as much a possible.

    Also genetics have a bit to do with likelihood for a pre-disposition for autoimmune disorders (not hereditary, just means your genes make you more likely to develop the disorder). For example, my father has leaky gut, and I have developed some autoimmune conditions (seasonal allergies, rosaecea, and sensitivities towards certain pesticides).

    Also exposure to environmental and biological stressers (some chemicals and psychological stress) over time tax the immune’s system’s ability to fight off the bad bugs too. Which is why we may see outbreaks of symptoms periodically rather than all the time.

  • I follow this site with great interest, as it gives such good, solid advise. One thing I miss, though, is any reference to homeopathy, which can help to address many of the issues discussed. I realise that the subject is far too vast, and far too individualised, to broach when making general health recommendations, since it is never a one-size fits all prescription. Concerning gastrointestinal heath, though, there are some remedies that can be useful without having a full homeopathic consultation, especially when one has suffered from gut dysfunction after treatment: a range of remedies prepared from intestinal flora, called “Bowel Nosodes” – easy to look up on the net. They can help to regulate the intestinal flora, without the prolonged use of probiotics. Keep up the wonderful work, Deborah Collins

  • Hello,

    I am 24 years old and have been suffering from IBS-C for years. The past 2 years the pain and symptoms have really taken a turn for the worse and it is more debilitating then ever – forcing me to quit my job, etc. I tested positive for SIBO, with methane gas levels at 58 and have already taken 3 rounds of xifaximin, once with neomycin which seemed to help for a couple of days during the treatment and now, finishing the antibiotics today I am the same as when I started. I just started the SIBO specific diet which include no dairy, grains, nuts, beans, or legumes. Does anyone have any suggestions or advice? Has anyone with constipation know of a great probiotic – not sure which one to try. Thank you!

  • What do you think about regular ingestion of apple cider vinegar with the mother strain for gut health? It has helped me since having two c sections.

  • I am 59 years old and 5 years ago was diagnosed by my very progressive internist with H Pylori. My symptoms were a pain above abdomen and below esophagus ,a lot of burping and panic attacks out of nowhere. My father was dying at this time as well, but I had never had panic attacks. She gave me a blood test, it came back positive and she gave me antibiotics.The pain remained, she unfortunately had moved to another city so I went to a traditional gastro doc and with great reluctance he gave me another test for H-pylori and a different antibiotic when it was positive. Awhile after taking the second round and the area was able to heal the pain went away. 2 months ago, the burping and anxiety returned and now I am beginning to have reflux I think. I know when I go back to the Gastro doc, he will prescribe antacid drugs. I have been meditating and the anxiety is disipating and I had read Juengers book Clean Gut a year ago. My diet has alway been pretty clean and after reading his book we have been gluten free for a year. Aside from using DGL before meals and taking Glutamine can you suggest anything else that I can do on my own.

    • Hi Claudine,
      Thank you for your interest In Dr. Hyman’s work. Unfortunately he cannot provide you personalized medical advice in this forum. In order to provide you the proper care you need we hope you will seek the attention of a local qualified Functional Med practitioner soon. To locate a doctor near you who practices functional medicine like Dr. Hyman, go to and scroll down to where it says “locate a practitioner” and enter your location. Progress accordingly from there.
      Wishing you the best of health,
      Dr. Hyman Staff

  • You said that “Symptoms throughout the body can be resolved by treating the Gut” and I think that’s the reason why it is said that Drinking plenty of Water daily can keep you out of various diseases and help remain healthy.
    It helps maintain the balance of body fluids and normal bowel function, help control calories, helps your kidneys, helps energize muscles and many more.

  • I have been eating clean since the end of November, and I want to take the best quality probiotic I can, could you recommend a particular probiotic/brand?

  • I’m confused by these five steps because in other places Dr. Hyman advises to limit flour and starch products, and encourages eating lean animal meats.

  • I have asthma nod I was wondering if anyone knows how to cure it without using meds ? I know all the medications can and do harm your body.

  • What about brain problems … OCD??? would love to find what to do for that. …we feel this is from brain injury… demerol shot… and before that vaccine damage.. .. any thoughts?? Will travel anywhere if this can be addressed… THANKS!!

  • sorry for the huge story but…recently 3 weeks ago now… when in the Phillipines – i had a bout of something like flu that lingered for 2 weeks or so and out of desperation i tried augmentin amoxycilin antibiotics -readily available over the counter – i realise they don’t treat virus but i got better in a bout 3 to 4 days… and then i got food poisoning from some chicken under cooked, i had 1 week ill very bad… dehydration and fever too, i got better and low and behold i went out and ate some crispy tuna belly and after eating some i noticed it smelt on my fork too late after i swallowed..1 week again sick and bad… and then better. so i thought… this was almost 4 weeks of illness… i took more antibiotics… and got better after around 3 days – but then 2 days later was very ill again and yes more chicken – and yes under cooked… but this time i was very ill and admitted to hospital… essentially what i had done was killed off all the good bacteria and bad… and yeast was in my gut and too over – food in my gut was decomposing… and had to pass through and i can tell you do not want to experience that – if you ever smelt a dead corpse that makes you throw up when you smell it – this is what is inside the gut… the side effects i had joint pain that stopped me bending down or using my hands, terrible pain in the head and brain pain, depression even delirium, i was at one ready to die and expected to and was actually ready for it – even wanted it as my state was pretty bad and i had enough of sitting for hours at a time in the bathroom even sleeping in it…but did actually wake up the next day and help came eventually, and so treatment, on my own i couldn’t move and didn’t realise i was in fact starting the path to die from dehydration… i could not keep the water in my body – i lost 10kg in weight – the hospital saved me from renal failure with a drip and 4 nights of treatment.. immodium was used to halt the constant gut action… i was worried about that but it did keeping all that poison in me… but it was the only way to allow me to keep hydrated for 3 to 4 days after being released… i was prescribe bland food, meat and vegetables only, no alchohol, no coffee, no dairy, no bread , nothing yeasty… and about 1 week after release from hospital, drinking chicken and vegetable soup with noodles only – i was able to stand up and move around… and 1 week after that i was getting back to normal – they prescribed me vials of acidophilus for 3 days also. Yakult was not the job for this. i needed proper medical grade probiotics. I totally agree with everything you say above and i have changed my life now due to me experience and eating super muesli for breakfast, i am eating vegetables every day.. and smaller quantities of meat.. .and yes probiotics and a low yeast type diet from now also… my only doubts are that retail probiotics contain dairy or the culture is dead, yakult was about the only dairy/yoghurt type probiotic that actually contained any living culture at all in a EU test about 5 years ago… anyway i agree and never again will i do that! i love this website it speaks the truth.

  • what I’m looking for which is someone who studies the gut n find all of the triggers that cause the gut to do what ever it does sorta like a gut genome..

    so maybe if this was done they would actually know why irritable bowel does what it does in others words if trigger A is on then the gut will run in “diarrhea mode” .. this is where I feel all of the researchers are wasting their time and making no progress. they should be mapping the gut cause and effects like they did with the whole gene system.

  • Hi, for many weeks I’ve been looking for remedies for my fiance. We are in a personal drought with bills, medical even but my fiances health is worsening. A couple years back he fell from a 43 foot roof, from he accident his veins began to purtrude from his legs and cause him crutial pain ever day. For the past couple weeks his stomach has been hurting and pain shoots to his back to me it sounds like a bacterial infection , him being in pain from his fall with this added upon him I just want to help . Can you give any advice upon treating an I’ll stomach it will be highly appreciated thank you
    Sincerely yours
    Rebecca Mcnemar

    • Hello Rebecca,
      We recommend that you seek immediate medical care for your husband. For diet, choose whole foods such as lean proteins (organic poultry, wild caught fish), vegetables, fruit, nuts, seeds, and gluten-free whole grains such as rice and quinoa to help him gain his strength back.
      Wishing you both the best of health,
      Dr. Hyman Staff

  • My 16-month-old granddaughter was recently bitten on her face by the family dog. There were two
    puncture wounds and surface abrasions. The pediatrician recommended ten days of augmentin. Obviously this will have an effect on her gut microbes. What do you recommend to help bring her gut back into a healthy balance?