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

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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

References

(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.

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

  1. Johanna July 10, 2013 at 1:04 pm #

    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?

  2. Stephanie Robbins July 10, 2013 at 3:30 pm #

    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?

  3. Carol July 10, 2013 at 9:33 pm #

    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.

    • Steve July 21, 2013 at 11:56 am #

      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.

    • Karen Berger December 4, 2013 at 11:47 pm #

      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.

  4. Jeff Swanson July 10, 2013 at 10:05 pm #

    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. http://en.wikipedia.org/wiki/Kefir

    • Johanna July 11, 2013 at 1:01 pm #

      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.

      • Gina July 21, 2013 at 4:18 pm #

        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!

      • Carrie August 13, 2013 at 9:40 am #

        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.

    • Cheryl November 13, 2013 at 11:41 am #

      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.

  5. janen July 21, 2013 at 5:46 am #

    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!

  6. Avatar of Barbara
    Barbara July 21, 2013 at 7:15 am #

    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….

    • Catherine Sullivan August 14, 2013 at 2:41 pm #

      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.

  7. Karen July 21, 2013 at 10:34 am #

    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!

  8. Belle July 21, 2013 at 2:44 pm #

    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.

  9. Emily July 27, 2013 at 11:32 pm #

    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.

  10. John G Martin August 9, 2013 at 1:47 pm #

    I have Parkinson’s. Can re-balancing your gut flora help with Parknison’s symptoms?

  11. Phil Lapp September 4, 2013 at 4:57 pm #

    http://www.eatneat.com! Nuts, Beans, and not much more!

  12. Myriam November 10, 2013 at 9:49 pm #

    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!

  13. Avatar of Adlet Nkiwane
    Adlet Nkiwane November 17, 2013 at 8:49 am #

    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.

    • Avatar of Team Hyman
      Team Hyman January 2, 2014 at 5:03 pm #

      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:http://www.bloodsugarsolution.com/nutrition-coaching/ OR call (800) 892-1443 to get started.

  14. jack mccarren November 26, 2013 at 9:00 pm #

    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

  15. Lynda December 12, 2013 at 8:02 pm #

    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.

    • Avatar of Team Hyman
      Team Hyman December 27, 2013 at 2:21 pm #

      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 http://www.functionalmedicine.org/practitioner_search.aspx?id=117 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: http://www.ultrawellnesscenter.com/becoming-a-patient/
      Did you know you can work with Dr. Hyman’s nutritionists virtually? For personalized nutrition coaching, please see: http://store.drhyman.com/Store/List/Coaching-Programs
      In Good Health,
      Dr. Hyman’s Wellness Staff

  16. Is there a specialist in Louisville ky December 30, 2013 at 10:00 pm #

    Is there a specialist in Louisville ky

  17. Mr. U January 7, 2014 at 1:42 am #

    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 !!!!!

    Regards
    Mr. U

  18. Dave Hayes March 30, 2014 at 3:16 pm #

    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

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