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What Causes SIBO (Small Intestinal Bacterial Overgrowth) and Why It’s so Hard to Treat


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Reviewed by Vanessa Wong, MD

While bacteria are an essential part of a healthy small bowel and perform important functions, small intestinal bacterial overgrowth can lead to leaky gut and a number of other symptoms. Learn what puts you at risk for SIBO.

sibo info
SIBO (small intestinal bacterial overgrowth) is a complex issue. istock.com/frentusha

The normal small bowel, which connects the stomach to the large bowel, is approximately 20 feet long. Gut microbiome bacteria are normally present throughout the entire gastrointestinal tract, but in varied amounts. Relatively few bacteria normally live in the small bowel (less than 10,000 bacteria per milliliter of fluid) when compared with the large bowel, or colon (at least 1,000,000,000 bacteria per milliliter of fluid). And, the types of bacteria normally present in the small bowel are different from those in the colon.

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Why You Should Thank Your Small Bowel and the Beneficial Bacteria That Live There

The small bowel plays an important role in digesting food and absorbing nutrients. It is also an important part of the immune system, containing an impressive network of lymphoid cells (cells of the immune system that help fight infections and regulate the immune system).

Are you at risk for small intestinal bacterial overgrowth? Find out what the most common risk factors and symptoms are.#SIBO #SIBOsymptomps

The normal (beneficial) bacteria that are an essential part of the healthy small bowel also perform important functions. These beneficial microorganisms help protect against bad (i.e. pathogenic) bacteria and yeast that are ingested. They help the body absorb nutrients, and also produce several nutrients (such as short chain fatty acids) and vitamins like folate and vitamin K. These bacteria help maintain the normal muscular activity of the small bowel, which creates waves that move the contents of the intestine, like food, through the gut.    

What Is SIBO?

SIBO, small intestinal bacterial overgrowth, is defined as an increase in the number of bacteria, and/or changes in the types of bacteria present in the small bowel. In most patients, SIBO is not caused by a single type of bacteria, but is an overgrowth of the various types of bacteria that should normally be found in the colon (1). Less commonly, SIBO results from an increase in the otherwise normal bacteria of the small bowel. 

SIBO has been shown to negatively affect both the structure and function of the small bowel. It may significantly interfere with digestion of food and absorption of nutrients, primarily by damaging the cells lining the small bowel (the mucosa). Additionally, this damage to the small bowel mucosa can lead to leaky gut (when the intestinal barrier becomes permeable, allowing large protein molecules to escape into the bloodstream), which is known to have a number of potential complications including immune reactions that cause food allergies or sensitivities, generalized inflammation, and autoimmune diseases (2).

These pathogenic bacteria, whether too many or the wrong types, can lead to nutritional deficiencies on top of those due to poor digestion or malabsorption. In particular, the bacteria will take up certain B vitamins, such as vitamin B12, before our own cells have a chance to absorb these important nutrients. They may also consume some of the amino acids, or protein, that we’ve ingested, which can lead to both mild protein deficiency and an increase in ammonia production by certain bacteria. (We normally produce some ammonia daily from normal metabolism, but ammonia requires detoxification, so this may add to an already burdened detoxification system.) The bacteria may also decrease fat absorption through their effect on bile acids, leading to deficiencies in fat soluble vitamins like A and D.

What Causes SIBO?

The body has several different ways of preventing SIBO. These include gastric acid secretion (maintaining an acidic environment), waves of bowel wall muscular activity, immunoglobulins in the intestinal fluid, and a valve that normally allows the flow of contents into the large bowel but prevents them from refluxing back into the small bowel. (This is called the ileocecal valve because it’s located between the ileum, or terminal end of the small intestine, and the cecum, a pouch forming the first part of the large bowel.)

The cause of SIBO is usually complex, and likely affects more than one of the protective mechanisms listed above. A number of risk factors for SIBO have been identified, with some of the more common risk factors listed below.  For a more complete discussion of associated diseases and risk factors check out this study and this study.

Risk Factors for SIBO

  • Low stomach acid
  • Irritable bowel syndrome
  • Celiac disease (long-standing)
  • Crohn’s disease
  • Prior bowel surgery
  • Diabetes mellitus (type I and type II)
  • Multiple courses of antibiotics
  • Organ system dysfunction, such as liver cirrhosis, chronic pancreatitis, or renal failure

Moderate Alcohol Consumption and Oral Contraceptive Pills (OCPs) Also Increase the Risk for SIBO

Heavy alcohol use has long been recognized in association with SIBO (3). This study also found an association between SIBO and moderate alcohol consumption, defined as up to one drink per day for women and two drinks per day for men. Alcohol appears to have effects on several of the normal protective mechanisms, including causing injury to the small bowel mucosal cells, contributing to leaky gut, and decreasing the muscular contractions. Additionally, alcohol may “feed” a few specific types of bacteria contributing to overgrowth (4).

Overall there appears to be a moderate association between OCPs and inflammatory bowel disease (IBD) such as Crohn’s disease (5). Though no studies to date specifically correlate the use of OCPs with SIBO, given the known relationship between IBD and SIBO, it is likely that this association holds true for SIBO as well. However, once patients stop taking OCPs, this risk appears to reverse.

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How Do You Know If You Have SIBO?

The number of people with SIBO in the general population remains unknown. Some studies suggest that between 6 to 15% of healthy, asymptomatic people have SIBO, while up to 80% of people with irritable bowel syndrome (IBS) have SIBO (6). 

SIBO is largely under-diagnosed. This is because many people don’t seek medical care for their SIBO symptoms, and because many doctors aren’t aware of how common SIBO is.

Complicating this, the most commonly used tests (breath tests measuring levels of hydrogen and methane gas) still have fairly high rates of false negatives (meaning the test results come back as negative but you actually do have the disease) (7).

The most common symptoms of SIBO include:

  • Abdominal pain/discomfort
  • Bloating and abdominal distention
  • Diarrhea
  • Constipation (generally associated with methanogens as Chris discussed in his recent podcast)
  • Gas and belching
  • In more severe cases, there may be weight loss and symptoms related to vitamin deficiencies.

Is SIBO Contagious?

Unlike many other bacterial infections of the gastrointestinal tract, SIBO is not contagious, and there is no evidence that exposure to any single microorganism increases the risk for developing SIBO. SIBO occurs due to a complex interplay of many different factors and is not passed on between individuals. However, some evidence suggests that there is an association between Helicobacter pylori and methane production, suggesting that H. pylori plays a role in gut dysbiosis. (8)

Why SIBO Can Be Difficult to Treat

Antibiotics are often used to treat SIBO. However, studies show that despite treatment with antibiotics, recurrence develops in almost half of all patients within one year. One study comparing treatment with rifaximin (the most commonly used antibiotic for SIBO) and botanical antimicrobials showed slightly better outcomes with the botanical protocol, but still with successful treatment in close to only half of all patients after one course of treatment.

These finding suggests that treatment of the overgrowth alone is not enough for most people. An additional piece of successful treatment must include addressing the underlying cause, or predisposing factor.

Though there are many identified associations between SIBO and other diseases as described above, abnormalities in gut motility are recognized as one of the most common associations. One study published this month demonstrated that patients with SIBO do have significant delays in small bowel transit time (the amount of time it takes something to move through the small bowel). This finding suggests that patients with SIBO, who do not recover after a standard course of antibiotics, or botanical antimicrobial protocol (which we prefer), may benefit from the addition of a prokinetic agent, which increases the muscular contractions of the small bowel. Octreotide and low dose naltrexone are two such options that are being investigated, and may help treat some cases of SIBO that don’t respond to antimicrobials alone. Other options may include prucalopride and low-dose erythromycin, as well as lubiprostone. (9)

As research into SIBO continues, we are increasingly understanding the complexity of this disease, and how treatment must be tailored to each individual to maximize success.

If you need support in dealing with SIBO, consider working with the California Center for Functional Medicine. CCFM offers a membership-based health transformation service that excels at helping people with chronic conditions make the changes necessary to reclaim their health. Find out more about what CCFM has to offer.
Amy Nett

About Amy:  Amy Nett, MD, graduated from Georgetown University School of Medicine in 2007.  She subsequently completed a year of internal medicine training at Santa Barbara Cottage Hospital, followed by five years of specialty training in radiology at Stanford University Hospital, with additional subspecialty training in pediatric radiology.

Along the course of her medical training and working through her own personal health issues, she found her passion for Functional Medicine. She works with patients through a Functional Medicine approach, working to identify and treat the root causes of illness. She uses nutritional therapy, herbal medicine, supplements, stress management, detoxification and lifestyle changes to restore proper function and improve health.

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Join the conversation

  1. Prescript-Assist is recommended as a better probiotic for SIBO. I notice it has prebiotics in the formula. I thought prebiotics were contraindicated for SIBO? Anyone know about this? Thanks!

  2. Great information! I can relate so much with everyone’s comments. I was diagnosed with SIBO 2 years ago after 10 years of misdiagnosed symptoms. I’ve tried many diets & medications that didn’t work and surgery to remove a portion of my colon. A year ago, I was introduced to a nutritional cellular cleansing program that has changed my life! Since starting this program my symptoms have reduced significantly (1 flare up in a year) and I feel better than I have in years, The program I’m doing is gluten free, soy free, non gmo, easily digestible, 99% lactose free and is convenient and easy to follow. I’m now on a mission to help others who suffer from SIBO and other gut related and autoimmune diseases. Email me if you’re interested in some information, [email protected]

    • This same diet is working for me so far, based on advice from a doctor who specializes in it.

      No booze, dairy, gluten, soy, oats, or GMOs.

      All the meat (i eat TONS of meat), eggs, vegetables, fish, potatoes (even french fries), rice, and fruit you want. I occasionally have a regular soda, but diet isn’t good for it.

      I used to be a moderate drinker but even with one drink now I feel the bacteria feeding on it.

      My doctor said after 3-4 months of this I should be able to have a drink or two without side effects.

      • And I take a digestive enzyme with my meals called Digest Gold. I also bought a bunch of other vitamins and pills based on my own research, like a multi, b-12 drops, and lots of PRIOBIOTICS in capsules. You need to replenish your good bacteria.

        If anyone has questions comment in this thread and I’ll do my best to get to you.

        • Brian, What kind of probiotics are you using. Has a SIBO knowledgeable healthcare professional recommended them to you? Thx.

          • My SIBO doctor recommended orthobiotic by orthomolecular. I’ve been taking that plus some other ones I got at the store. Capsules tend to keep live bacteria better than hard pills. The exact diet he recommended to me is low FODMAP (look it up) and no alcohol. I also did a 13 day cycle of Flagyl initially because my pain and bloating was so bad I couldn’t get out of bed.

            • Bryan,
              I’ve been on the FODMAP diet, enzymes and nutrients, also Cod Liver Oil, Gentian and Skullcap and BioTonic. I still get very bloated. Which probiotics to take is confusing. Elaine G. who wrote the Breaking the Vicious Cycle book prefers the homemade yogurt only for probiotics, secondly LactoAcidophilus. I’m having a heck of a time finding “safe” acidophilus. I’ll check into what you are taking. Right now been using LactoPrime and got some VSL#3 which I used to take all the time. Thanks, let me know more details on any of the things you take if you feel comfortable sharing. (Like: who is the SIBO doctor that you see?)

      • Bryan….I would like to try this diet. Do you have information on it? However, I can’t eat most fruit at this time.

        • Tiffany, what are your symptoms when you eat fruit? No one says what their symptoms actually are. Most fruits give me bad breath and make my teeth and gums hurt, but I haven’t found anything linking this to SIBO that others have in common. Not very many if my symptoms match SIBO, but I tested positive only at the end of the test. Body aches are the primary complaint I have and no one can figure out why! but it’s definitely made worse by eating sugar, yeast, most fruits, vinegars, alcohol and most sweet fruits.

          • Cheryl,
            When I eat most fruit, I immediately…and I mean within 30 second…swell HUGE. You can actually see it happen. My stomach feel uncomfortably full even if I eat one bite. I am usually on the floor for an “episode”…as I call them…for about 20 minutes. Stomach pain….more burping than you can imagine…and after a while it will settle down. However, the swelling usually lasts for hours upon hours. Before I was treated with the antibiotics, one the swelling happened it did not go away until I woke up the next morning. I do not have any of the symptoms that you describe regarding my gums or body aches. I am curious to try the water though. It is working for you? How long did it take to see results?

          • I heard Dr. Siebecker (SIBO specialist) mention that an immediate reaction like that can mean yeast. Which could mean you are dealing mainly with yeast overgrowth or a combination of SIBO and yeast overgrowth. Most of the foods you listed are the same foods to be avoided when you have yeast overgrowth. You may want to check out my blog, because I have dealt with both yeast and SIBO. (www.familyhomeandhealth.com)

            • Thanks Kristie. And how did you treat that? Yeast Overgrowth. I think I was tested for that and it was negative? I could be wrong. I was tested for everything under the sun for over a year. I even had exploratory surgery. Nothing…

              • I was tested for yeast through lab tests that are done at home and mailed in. I think it was through Metametrix Labs. I also later realized that mercury toxicity was part of the problem. Yeast goes hand in hand with mercury toxicity.

            • Oh yes, it’s definitely yeast. Yeast that no one believes exists or argue with you about. I’ve eliminated all the foods that feed it, and taken every anti yeast protocol that I can find! and there aren’t many people who will actually post a protocol online. They all want you to pay to be a client first. But I out together my own concoction of about 10 different things including caprylic acid, was super strict and didn’t eat anything that feeds yeast, and I did it for 2 months straight. By the end, my butt was so sore from irritation, but I felt good besides that. Then I Accidently ate something fried in canola oil, a no no for yeast, and EVERY body ache (my 13 year symptom) came back. I have been on that strict diet for over 2 YEARS now!! Whatever is in my gut will feed on ANYTHING to survive, and I can’t find a protocol that works or someone who understands it in the drug company infested state of NJ. Prescript Assist is the only probiotic that doesn’t make me achy. SIBO is supposedly a cause of a achiness, but after the treatment, I didn’t feel even the slightest bit different.

    • have had digestive problems for years. Have gotten to the point that I don’t have a glue of what to eat . Had many test. All negative. Going to test for sibo again. Help

    • I would like to know the details of your diet. It sounds as if it is working for you. I see a gastroenterologist in Boston. I was diagnosed with SIBO last year. I have been on Flagyl twice due to the fact that my insurance is rejecting payment on Rifaximin. I have lost twenty pounds in the last seven months and feel awful pretty much on a daily basis. I am happy when I hear of anyone who is having relief from this problem. I am at the point now that I am going to start working sitha nutrionist.

      • Hi….I have struggled for almost two years. Traveled to Mexico healthy returned sick. Many tests and doctors later my new doctor who is a natural path diagnosed me with SiBo. She prescribed rifaxian my insurance would not cover the whole amount. So I went to rifaxian.com for a discount card. You will only pay 10.00 for prescriprion. 🙂

  3. Hi
    I can’t find a doctor to know much about sibo. After taking 30 days of Xifaxan and 30 days of Cefalexin with only 20% of improvement, my doctor now wants me to try Flagyl. They test for hydrogen only because don’t have the meter to test for methane. I now quit taking antibiodic, just self treatment with Neem Plus, Allimed and Lauracidin. Should I also take digest enzyme to help because I have so much gas pain, bloating, indigestion and constipation. Could anyone please let me know a good digest enzyme that I can take now? Thank you very much!

    • A Naturalpathic doctor recommended Integrative Therapeutics Similase GFCF, 120 Veg Capsules. I take 3 with each meal. You can find it on Amazon.

    • I use Integrative Therapeutics Similase GFCF. There is one that is better for those who need help with Fat Absorption which I’m going to look into. The Integrative Therapeutics site may be able to help you figure out which is which – I’m still figuring out myself. My naturalpath recommended this brand.

    • I am sure there are others but Jill Carnahan near Boulder and I personally have had good help from Nita Desai in Boulder though her approach is Ayurvedic.

      • Thanks, LM. I’d love to chat off line. Do you know if there is a way to share email addresses without sharing with the entire group. Thank you so much for responding so quickly. Much appreciated.

        • No Problem Jean, I just happened to be online today and refer some people that live in CO, my old home. You can find me & address at w.redhorsewellness.center . 🙂

    • Hi Jean, I live in Denver and go to Denver Digestive Health and see Daniel Siegel. He dx’d my Barrett’s Esophagus and my SIBO. I work closely with him to keep it under control, but unfortunately mine has been very stubborn and I have been on 3 rounds of antibiotic (Xifaxan) several times in the last few months. He is now talking permanent antibiotics, but I have to do another breath test next week first.

    • Alison Hoffmaster at Home of the Healing Arts in Erie Colorado. I have Celiac and SIBO. She has really helped me.

  4. Thanks for the great article. You mentioned LDN in your article , has there been any reports of elevated prolactin as a result of the use of that drug?

  5. i use braggs apple cider vineger! i have had this sibo! for 15 yrs!
    vinergar kills overgrowth for the bacteria! kills the gas in the intestines! better then antibiotis! i take 1tbsp ! a day! makesure it is cold you taste nothing! hot or room temp! is gross!

    • I”m confused when you say you’ve had this for 15 years. It doesn’t sound like your current treatment is working, or shouldn’t it have been gone ? like many years ago ?

  6. I have experienced many of the symptoms described by others and have been to doctor after doctor and had many tests. The one symptom I have had for 2 years now is a burning irritation in my mouth that no one can diagnose. I have not read where anyone has complained of mouth issues so I am curious if this is somethng anyone else has experienced in addition to the other symptoms of SIBO?

    • Hi Cindy,
      I have that from my GERD. I also get mouth sores. I take PPIs for it which also causes my SIBO. It’s been a vicious cycle for me.

    • Cindy, you might be dealing with candida/thrush. Your symptoms are common to candida and thrush. These conditions are often linked to other digestive challenges. It’s worth doing a little research on. About 2 years ago I had my amalgam fillings replaced to get rid of the mercury in my mouth and it made a significant difference for me. My tongue had felt burnt for years. It was a sensation you might experience after burning your tongue with a hot drink.

      • I had my amalgams out in 1991, developed burning mouth syndrome 3 years ago. It developed gradually over a week or so and has been permanent ever since.
        I have not been officially diagnosed with sibo, but almost certainly have had it for 37 years. I was diagnosed with Crohn’s on the basis of ulcers in my small intestine. I have taken multiple rounds of antiparasitic, antifungal and antibacterial herbal formulas. I have felt the die off symptoms each time and have had some improvement, but never been without symptoms. I am currently on a low fodmap diet and taking antiparaisitic herbs again. I am only now able to tolerate these herbs at a higher dose, having been unable to take more than a fraction of the dose for all these years. Still not on a full dose though.

    • I developed a mouth inflammatory ulser. Had to have it biopsyed. It was negative for cancer. They felt the sibo caused it. I now have burning tongue syndrome. Sibo has also returned. Unfortunately no cure for burning tongue syndrome

    • Cindy, You probably have Burning Mouth Syndrome. While there may be no cure for it, there are many things to help the symptoms. I have had it for 16 years. The one medication that made my symptom pain go from 9 to 1 (on a 10 pt. scale) is Savella. I have a great deal of info. about it; feel free to contact me.

  7. Hi everyone
    Please let me know what is the best way to take Allimed for sibo. I put 12 drops of allimed in my meal 3 times a day but someone told me that I should put the drops in water and drink it. I am confusing now. Thank you!

    • For three years I have on and off upper right abdominal pain. I have done all tests possible. I just t tested positive for sibo. The doctors look at me as I’m crazy. Does anyone else have attacks? Especially after they eat. This is horrible!!!! I am giving up. Always in pain, it’s just different ranges. Stomac talks to me with weird sounds.

      • Upper right is often liver and gallbladder related so you may want to add that to the list to get assessed for. Pain like that shouldn’t be ignored.

      • Ethel, I understand your suffering because I am going through so much upper abdominal pain which feels rock hard and very uncomfortable and difficult to breathe at times. When I lie down at night, my growling is non stop and makes it very difficult to sleep. It does seem to get worse with taking probiotics and I just listened to Alejandro Junger, MD on the free Healthy Gut Summit which started today mentioning this. I never heard of SIBO until I listened to that talk and found this article by doing a search. It sounds like what I might have because whatever I did to help this, didn’t help. I tried Aloe Vera juice, Dr. Friedlander’s excellent Ultra Blend probiotic that I heard from Dr. John Gray and other things. I have been on a gluten free diet for over 10 years and try to avoid GMOs like the plague. I do notice my stomach rumbling worse if I eat anything with GMO or Xanthum gum. I don’t feel like eating lately and so sick of my bloated and distended upper abdominal discomfort. Now I am listening to Dr. Galland talking about Gut, Brain, Bugs and Parasites. I feel like I have a family of something growing in there because at least it sounds like it.

  8. Been suffering years now from SIBO. Sometimes I feel like giving up, due to all my food intolerances (dairy, gluten, kale, eggs, onions, etc), strict diet, the fact I’m starving a lot of the time, chronic symptoms (bloating, diarrhea, rotten egg smelling burps and farts, etc), and so on. I’d just like to share some things that have helped: fasting a day or two, waiting 4-5 hours between meals ie no snacking, the Digestive Health Institute, and hobbies.

  9. I have had multiple abdominal surgeries and had a Dr. pull my intestines into a drain hole (that was cut too large) when removing the drain after one of the surgeries. They were stuck in the drain hole for 2 years and I had a lot of gastro intestinal trouble with multiple tests showing no issues during this time frame. It was exceptionally frustrating. Finally a Dr. found the issue during a Colonoscopy and a couple great surgeons repaired the problem in multiple surgeries (one to the remove the intestines and one to repair the incisional hernia). Afterward, I was in for a follow up colonoscopy and the Dr. told me offhandedly that I have SIBO and that it would most likely be an easy fix with a course on Xifaxan antibiotics. I was so excited to feel better and ended up taking two courses with great relief from symptoms but when not on the antibiotics the symptoms return quickly. I researched on my own and modified my diet to strictly follow a GAPS diet. I have quickly lost 38lbs and was hoping not to lose more but do have a lot of relief from SIBO symptoms while on the diet. I went back to the Gastro Dr hoping for more help and he told me that the enzymes needed to digest sugar/lactose/wheat and other foods were permanently destroyed in my systems and I should just follow a diet that “works for me” for the rest of my life. He wasn’t concerned with the weight loss, with giving me specific direction for diet, and said there is nothing else he can help me with at this time. He was very polite but I feel dejected about not knowing more about how to get better without losing more and more weight. I would really like to “heal” my guy if at all possible. I also have an issue with Osteopenia and need to consume enough calcium to keep my bones strong. I don’t know if I am doing the right things and feel like I am just taking guesses and it’s a shot in the dark if I am doing the right things. I have just starting reading all of your info posted as well as comments here. If you have any additional direction or information, I would really appreciate the help. Thank you.

    • Have you read about fecal transplant? It would restore the missing enzymes. Might also increase the good bacteria necessary to overcome the bad.

  10. Could someone please help me? I have bloating,constipation,all lot of gas especially in the upper stomach, a do i am pain, indigestion. For the pas 9 months I got several endoscopy,ultra sound, ctscan, ugi xray….All gi doctors that I saw told me to take PPI. No improvement after 9 months of ppi. I changed gi doctor again and did the latulose breath test. My chart for every 15′ is 12,31,30,29,48,27,48. They said I am positive and need to take Xifaxan twice a day for 1 month. I am on day 3 now and don’t see and different yet. I lost so much weight. 5’2″ and only 78 lbs now. I am so scare and don’t know what to do. I live in AZ and don’t find any dietitians/ nutritionist that know about sibo. How do you if you got methane or hydrogen bacteria because my gi doctor does not know? Thanks

    • Need Help, there is lots of good info here, I just want to add there are also a lot of holistic and functional medicine doctors, chiropractors, nutritionists and such in AZ. I travel from OH to AZ to be with some of them so I am sure if you keep searching you will find someone. Google holistic, functional and naturopathic medical associations and they usually have a directory for professional registered with them. I feel moved to tell you to keep in mind when you go to a new dr. YOU are interviewing THEM. If they don’t listen, seem to care and have some direction to start in they should at least direct you to someone who does. There are answers for you- don’t give up.

      • Thank you! Do you know any doctor, nutritionists, dieticians in AZ that understand sibo that you can recommend me? I Google and called a few but they are not familiar with sibo.
        Jennifer mentioned about medical food Entergram has helped her to get rid of sibo. Do you know or try it before. I wish Jennifer is still around here and tell us more about it. Thanks!

          • Thank you LM! I saw a couple that treat digest, gut problem. They don’t mention about sibo in their specialty. I will call them to find out. Thanks!

              • Hi Pitt
                Could you please give me his office phone number? Is he naturopath doctor Steven Bescak? Thanks!

    • Dr. Bescak in awahtukee is great. I have been to 3 gastroenterologists and none mentioned Sibo or feed allergies. I have bloating that’s lasts for days and days. This guy is the one that told me about sibo and tested my blood for food allergies. Come to find out I am allergic to wheat, corn, potatoes, strawberry, carrots, apple and oats; which he says are caused my the sibo. Going back for the next appointment to discuss treatment option. This has been a struggle and a depressing day to day. Bloathing everyday is wearing on me. When I take all these foods out of my diet I do see results, but it’s hard to do they add wheat and corn to everything! !!

      • Hi Pitt
        Thank you very much! Could you please give me his full name or phone number so I call to make appoinment? Hopefully he has an opening this week. Is he gi doctor? I Google around and find a family doctor name Steven Bescak so I am sure if he is the one. Please let me know. Thanks!

      • Hi Pitt
        Could you please give me his office phone number? Is he naturopath doctor Steven Bescak? Thanks!

    • I’m sorry to hear about your G.I. problems. Dr. John Wells in Phoenix 602.493.3030 is an amazing G.I. doctor. I and many others in the medical field including doctors prefer his guidance. I don’t know if he is familiar with acronym “SIBO”, you may want to refer to it as “small intestinal bacteria overgrowth”. You can ask the receptionist when calling if they can check with the doctor before you make the appointment, so nobody’s time is lost. You may want to take reputably sourced literature to appointment.
      I have been with Dr. Wells for more than a decade and have had four colonoscopies amongst other treatment. I actually get excited to see him. That being said, he is easy to talk with, takes the time to understand what you as an individual (patient) are experiencing, and has always fixed the problem. Best Wishes to you!
      ps – Almost forgot, Dr. Wells has also received Best Doc Award!

      • Thank you JR! I spoke to doctor Wells’s assistant. She said that doctor Wells can treat SIBO based on the symtom but they never do breath test so she is not familiar with the breath test for sibo. I have called a dozen of doctor offices in az so far (including intergrated and naturopath. None of them know about breath test for methane or treatment for methan. They either do only hydrogen test or just treat based on the symtom!!! I saw a lot of comment from this site talk about methane test, methane level or treatment. I feel that they are so lucky to find a doctor understand and know how to treat sibo properly. After changing gi doctors so many times I found a doctor that offer hydrogen breath test and put me on xifaxan for 30 days twice a day. I am on it for 15 days so far with no improvement at all. I think that I have nathane because of very bad constipation but I don’t know what to do because all doctor offices that I went to or call have no idea about it!!!

    • I also live in Az and see Dr. Nemechek. He is in Verrado which is actually in Buckeye. He specializes in SIBO. Give him a call he can help you.

        • Thank you very much, Lori! If you don’t mind please give me a call 480-242-3751 or I can give you a call if I have your number. I would like to ask you just a couple of question about your experience in sibo treatment with doctor Nemecheck.

    • I’ve taken Xifaxan several times and generally don’t start to feel better until I am almost done with the prescription.

      • Thank you Liz—I am on my 3rd episode of Xifaxin (over a 2yr period) and this time, I am on day 3 with little improvement.
        Your experience seems similar.
        This site has opened my eyes–FodMap diet and herbal + digestive enzymes seem to be the answer for many.
        Thanks to everyone for your comments!

    • Looks like after blood, stool and medical procedure tests I have SIBO because after 5 days of Xifaxin started having normal stool again after 5 mos. of unexplained dirrhea. Exctastic! Also started Fodmap diet at same time. By day 10 on Xifaxin bloating, gas, diarrhea returned. Devastated. Adhering to Fodmap diet closely now – will see what happens. Before 5 months ago never had problems with bowels – a literally just overnight change. I went on Fuhrman’s nutritarian diet a year ago to control cholesterol without medication and keep wondering if this has anything to do with problems I am having today. Any experience, strength or hope on this issue. Been great to find this community and know I am not alone.

  11. Tested positive for SIBO. I just finished a 30 day round of Xifaxan (Rifaximin) 550mg twice daily and have been prescribed VSL #3 twice daily for 30 days. I am still experiencing some heartburn, gas, bloating etc but not nearly as badly as pre- treatment. Can I take antimycobacterials such as oregano oil and berberine and perhaps a biofilm disrupter with Lactoferrin in conjunction with my prescribed probiotics? or will this cause problems? should I just continue a low FODMAPS diet and try to restore my good gut flora and retest for SIBO after my round of probiotics? What protocols should I be currently following?

    • Hi – I am going through a similar process at the moment and just wanted to say that taking oregano oil with probiotics is not a good idea. Oregano oil kills good and bad bacteria, it is thought, so will undermine the VSL’s progress. I’m not sure about berberine but I would give the VSL a chance first. It can take a couple of months for good bacteria to become established, apparently, so it might take a while for you to see improvements. However, you can try taking things to repair the gut lining at the same time without problems as far as I am aware. One of the best researched of these is colostrum – I have read a lot of stories with people saying this helped them with SIBO.

      I’m surprised that you still have heartburn after antibiotics. Have you been tested for H. Pylori? My experience has been that probiotics and antibiotics have gotten rid of problems higher up, so I’m only getting symptoms of bloating etc. lower down my abdomen now. It struck me as odd.

  12. Low FODMAP is a must for me. Reintroducing probiotics was the biggest mistake – all horrible symptoms came flooding back. Just my two cents.

    • Emily…I just started Plexus BioCleanse and ProBio5 to see if it would help me. Are you saying Probiotics made your symptoms worse? Please let me know. Thank you for any information you provide.

  13. After 30 years of struggling with a very sensitive gut, I was recently diagnosed with SIBO. I thought, “Really, I already knew this, but had no name.” So sugar and carbs hate me. Haven’t eaten red meat in 40 years. Live a pretty healthy lifestyle but do love my red wine and chocolate. Have a long term bout of this every year or so now, pretty chronic. So many things out there, currently on my second round of Xifaxin. Wish someone would just tell me what to eat and when!!!

  14. I had SIBO (and yeast overgrowth – I suppose it could also be called SIFO) diagnosed via Metametrix organix dybsiosis test. Per the Metametrix stool test from the same time period, I had slightly low levels of bifidobacteria and a parasite, Cryptosporodium, and some slightly high levels of Achromobacter/Alcaligenes – the test calls them opportunistic bacteria, I believe.

    My doctor advised to treat the yeast (but not SIBO) with Candibactin AR (60 capsules) and Candibactin BR (90 capsule bottle), and also was advised to use a homeopathic product from Emerson Ecologics, which I did not bother to use. For the Cryptosporidium I chose to treat with nitazoxanide, and also took Therbiotic Factor 4, a medical grade probiotic, to restore my levels of Bifidobacteria. I re-tested my stool about 5 months later, and it showed resolution of the parasite and bifidobacteria was brought up. About 10 months after the treatment, because I still had issues with brain fog, I re-tested via the Metametrix Organix urine test. It showed that my high levels of bacteria in my urine had resolved (i.e. my SIBO), but the fungal dysbiosis did not resolve. I later found out I had H. Pylori, which tested positive via blood antigen and stool antigen (BioHealth), but had never tested positive despite my two stool tests from Metametrix.

    I chose to treat the H Pylori and yeast via natural methods as well, including biofilm busting strategies, for about 2 months, while also supporting my adrenals.

    After all of this – I feel better, but my energy and sleep are still not where I would like or need them to be sometimes. I’m still on the adrenal healing protocol. I can now tolerate onions without gas! That’s progress, right? I think low FODMAP is still necessary for me, but I’m so tired of restricting foods.

    I also noticed a huge benefit from (I believe) Orthomolecular products for H Pylori and Candida- I saw better skin healing, and less PMS, and I think despite trying to include more seafood and beef liver I was copper toxic and zinc deficient (hair test for this was somewhat conclusive – copper was “normal” but zinc was kind of low, but I didn’t want to supplement zinc right away since it can exacerbate fungal infections, and I’m glad I waited to take zinc undecylenate).

    I have not taken a prokinetic, like LDN, but would be interested to try this, for help with energy and sleep.

    One of the things that’s not clear to me is resolving issues with FODMAPs. Do you really have to stay low on these foods for the rest of your life?

    • MP thanks for sharing all that precise info! On a long journey myself and have used some if the same tests you have but very helpful to hear someone else’s approach. I am in LDN but only 2.25 not the usual 4.5. I have not found it helpful at all with transit time but that us just my body. I do notice as long as I can sleep through the night it lessens autoimmune related swelling in some joints and actually acts as a bit of an antidepressant, an unexpected but appreciated ‘side effect’ for such a low, safe dose. Hope you share more as you progress! One thing I did not see anybody mention in comments or article is the effect of stress/ perception in recovery and prevention of reoccurence. I don’t think that can be underestimated! Best wishes to everyone 🙂

  15. Hello,
    I was wondering if you can recommend anyone in the Boston area for treatment of SIBO. Thanks!

    • Albena halbert or tony lembo. Referred to me as top GI drs by Doug drossman at UNC. GOOD LUCK

    • Dr Gordin at Merino Center in Cambridge, MA is treating me for SIBO and leaky gut. I also have celiac. He will give you a breath test to take at home and mail in. Tests for both types of bacteria. Test is sent overnight to some place in So Carolina. He has me on a strict diet and a regime of herbs etc that he has prescribed and i can buy from a company who only sells to people with a Drs prescription. (I can’t do antibiotics.) He also has me doing acupuncture every 10 days or so. And working with a nutritionist. They have an acupuncturist on staff and many insurance plans in MA will pay for it. I’ve just started the regime (was just diagnosed) so i can’t say if its working yet. But i’ve been on the FODMAP diet for 4 months and he says that has probably helped me a lot. I feel a lot better on FODMAP, but still have issues with bloating, etc bc of the SIBO. And LOTS of food allergies/sensitivities bc of the leaky gut.

  16. Receiving a diagnosis has been the battle for me. I am a 28 year old male who has been trying to find a diagnosis for 5 years for my ongoing stomach issues; most of which were mentioned on here. I finally received a diagnosis of gastroparesis after having a gastric emptying study but unfortunately they do not want to look into SIBO being associated with the gastroparesis. It has been very difficult the past 5 years but I have that I will eventually beat this thing. Prayers for anyone else out there struggling to get a correct diagnosis.

    • How did your gastoparesies start and how did you manage weight I have been struggling with the same issue no amseer

      • I believe I have had the gastroparesis for some time however, I just went on with my day to day life not really realizing I had it. I had been to the gastroenterologist so often when I first developed symptoms, that I eventually stopped going when they kept throwing IBS medications at me that were no help whatsoever. Earlier this year, I began a paleo diet and after months of low carb, the gastroparesis got really bad. That is when I went back to the doctor, received the diagnosis and stopped the low carb diet.

    • Hi Geoff, I feel your pain. the diagnosis was the hardest part for me too. It costs a pretty penny, but I would highly recommend doing the tests that SCDLifestyle.com recommends (check out here: http://scdlifestyle.com/2013/03/are-unreliable-lab-tests-stealing-your-money/) – it’s now the doctor’s data x 3 parasite, BioHealth 401H (parasites + H pylori) – I think this one is over 4 days, and last but definitely not least, Organix Dysbios of urine. There is no perfect diagnostic test, but those will help you get a good amount of the way there, as well as troubleshoot gut bacteria deficiencies.

      Those guys suffered a lot and trained with Dr. Kalish. I have benefited from their wisdom, and I’m a *LOT* better than I was.

      • sorry Dysbiosis – that was mispelled before. Also, an Adrenal BioHealth (I think it’s 205?) of DHEA and Cortisol if you have any kind of sleeping problems….

        • I convinced my Gastro to test for SIBO and I just received the results today. It turns out my Hydrogen count was quite high while my methane count was normal. So, now I am just waiting to hear from my Dr. as to what the next step will be. I am familiar with SCD lifestyle but honestly, the more I read and educate myself about the issues I have with my digestion, the more stressed and tired I get. I have put it in God’s hands and I pray that He helps me recover. Of course, good decision making on my part is a big part of that process. I remain hopeful though.

          • Hi Geoff,

            Have you checked out siboinfo.com? Also underground wellness with sean croxton had a really great session about sibo. if you leave an email, I can send you the pdf about it. it talks about how anything above 3 ppm for methane is considered positive for sibo, and that’s kind of cutting edge. before they were saying anything above 12 ppm was positive, and anything below 12 was negative! and hydrogen anything above 20 million ppm is positive.

            might want to look at your test results, in case your doctor doesn’t know.

            also, if you have both methane and hydrogen, you have to take both rifaxamin and neomycin (I believe, not 100% sure). Rifaxamin is for hydrogen, but metronidazole or neomycin is necessary for killing the methane organisms.

            Anyway – my two cents – I’m glad I didn’t do the antibiotic route because I feel like that could set you up for recurrence. Knock on wood I haven’t had recurrence yet

            I didn’t do the breath test, just the organix urine dysbiosis test, so unfortunately my SIBO numbers on hydrogen and methane are not as good, but I like the measurement of SIFO (small intestinal fungal overgrowth) which I suspect is present in a lot of cases where the SIBO symptoms don’t resolve. it’s less common but I would imagine, also exacerbated by a paleo diet and the increased amount of saturated fat one begins to eat, in addition the FODMAPs.

            But then, everyone is sick in their own way. god bless – good luck!

            • I have checked out siboinfo.com and got a lot of good information off of their site. I would prefer to go the natural route with treatment but I have not had any luck doing so in the past. So, I think that antibiotics are the next course of action. I will post once I find out the treatment plan.

  17. I’m suck , I can’t eat meat, or veggies and now fruit is causing me problems. Can Chris help, I can’t just start eating Paleo , I can just barely eat some fruit and sweet potatoes, that’s it. no rice, no pasta, no meat, fish is ok but worried about to much mercury with everyday consumption, what can i eat?

    Multiple Antibiotics as a kid for sinusitis (probably 5 times total)
    1991-1996 Antibiotics 2-3x per year for sinusitis
    Gallbladder removal 1998 (by accident)
    1998 had rashes & dandruff in mustache, ears and eyebrows (now know it was caused by eating simple carbs or night shades) continued for years still present, resolves with adequate sunshine daily.
    2004 started drinking Alkaline water from one of the electric machines (for general health)
    2006 started having digestion problems in form of face blemishes
    2006 started taking digestive enzyme with meals, resolved the blemish problem
    2007-2011 need for enzymes increased to include HCl, cannot eat fats, plant oils, avocado, some meat fat OK
    2012 all meat Paleo type diet with sauerkraut for a year, cholesterol got to high, blemishes
    2012 digestion cured for about two weeks I could eat anything with no enzymes, i started eating lots of carbs, oatmeal, quinoa, brown rice, etc… digestion quit working after 2 weeks, never to return ( i was ignorant to why at the time)
    2012 got a severe sinus infection went through 3 rounds of 3 types of antibiotics to kill it.
    2012 got food poisoning twice in a row from eggs, really bad, 3 days each time nearly died.
    2013 inflammation, back pain, butt, leg, sciatica, neck, finally figured out it was meat, eating meat causes me inflammation within one day, even tingling in arms, fingers, complete EKG, Cardio, and Ultrasound, checkout at ER found nothing wrong.
    2013 gradually switched to vegetarian diet, juicing for many months, started having severe reaction to veggies, brain fog and worse
    2013 gradually switched to fruitarian diet, the only thing i can eat is fruit (no enzymes required) 25-30 bananas a day, apples, peaches, etc.. felt great, super energy no pain, very limber, working out, all great.
    2014 fruitarian diet, eating meat 2-3 times a week, meat still causes inflammation, added sweet potatoes,
    2014 Oct, after eating red wine vinegar had severe reaction, eye went blurry for hours, digestion regressed.
    2014 Nov, still can’t recover from Oct, getting dizzy and Brain Fog from fruit, still can’t eat meat or greens, sweet potatoes cause gurgling in lower intestine but no other reactions

    • Holy smokes, Joseph. That’s alot! But sounds just like me. My problem is I can’t seem to pinpoint a certain food that triggers me. It doesn’t matter what I eat or don’t eat, I get tons of bloating, gas and PAIN. All of this is so old, I am so tired of it. I was diagnosed with SIBO and Barrett’s Esophagus. No real answers yet. Having another breath test next week and my Dr is now saying I may need to be permanently on antibiotics.

    • Joseph, did you ever figure out what was wrong? My history looks a lot like yours minus fruitarian and i’m confused about what to do next

  18. I have a rare form of leukemia known as Chronic Lymphocytic Leukemia (CLL) which has led to the decline of my immune system. I got diagnosed after having severe intestinal symptoms, including severe weight loss and diarrhea. I have had every test known to mankind and have left every gastroenterologist scratching their heads about my symptoms. I had the SIBO breath test and it was negative. Over the past four years I have cut out all wheat and nearly all dairy. My symptoms have improved but I still suffer bouts of diarrhea, gas, bloating, and sometimes even incontinence. It’s awful! I have finally diagnosed myself with SIBO. How? After a round of antibiotics for an infection (and I get them regularly with my suppressed immunity) I have a marked improvement in my symptoms, but after stopping the antibiotics within months, or even weeks, my symptoms return. The light finally went on for me when I was reading an article about SIBO and it said that frequent bouts of SIBO will cause blunting of the villi similar to Celiac Disease. I had a capsule endoscopy that showed exactly this and the doctor couldn’t come to any conclusion. Since I can’t seem to find a doctor that will help me with my intestinal issues (and I have been to many good doctors in Southern CA, including some at UCLA), I have been reading more on my own. I am reluctant to take antibiotics regularly as I fear becoming resistant to their benefits, and I will likely need them more as my disease progresses. I have immunoglobulin treatments monthly to boost my immunity. I have found in my experience that probiotics make my symptoms worse and I have had mixed results with FODMAP and similar diets. I do have some improvement with adding digestive enzymes to my diet, and ant-gas tablets help, too. I need more permanent relief. This is severely inhibiting my regular lifestyle. I appreciate reading what has helped other people. I am especially interested in the EnteraGam that another person wrote about. Now I need to find a doctor I can work with in the Los Angeles area who really understands SIBO and it’s link to suppressed immunity.

  19. Agreed. How about utilizing Triphala as a prokinetic agent? And perhaps other botanical medicines?

    • I had that same question re triphala!
      I can see that’s another place where caffeine comes in also. So many things I think of as “prokinetic” have negative consequences or build tolerance.

    • Yes, and in addition, one of the three ingredients that make up Triphala ( Terminalia Chebula) contains Anthraquinones in the pericarp of the fruit. Anthraquinones are known laxatives, but they are also known to inhibit Methanogenesis and so reduce the formation of Methane gas in the Colon (they also inhibit formation of Hydrogen Sulphide gas by inhibiting Suplhate reducing Bacteria). Perhaps this is another mechanism of action and also the reason why Triphala is contra-indicated in Crohn’s Disease.

      • Hi.. what you said about Triphala is very interesting. It seems to be a good thing, no? Inhibiting hydrogen gas… can you please clarify?

        • The Gut flora is responsible for converting the remains of undigested food and mucus into small molecules that appear to have properties that directly affect the health of the Host. Some of these microbial metabolites have beneficial action and others are known to have a deleterious effect on the functioning of the body. A good example would be the short chain fatty acids Butyric, Acetic and Propionic acids which have properties that affect metabolic pathways involved in energy creation and also appear to affect gene expression by acting as signalling molecules.(good?) Another example is secondary Bile acids.(bad?)
          The final products of Carbohydrate fermentation in the Ileum and Colon appear to be Hydrogen and Methane and it is thought that this pathway drives the other microbial fermentation pathways.
          Methane appears to be associated with conditions that present constipation as the main symptom. (IBS-C)
          Hydrogen appears to be associated with conditions that present Diarrhoea as the main symptom (Crohn’s, UC)
          It is possible that the ratio of Hydrogen to Methane may determine Gut motility .
          Gut motility is responsible for moving the contents of the gut forward (in addition to mixing and Churning of food particles for digestion and absorption and creation of faeces or Stool in the Colon) The “house keeping” persitaltic waves (migrating motor complex) are responsible for clearing out undigested food particles and microbes out of the Stomach and small intestine. Failure of these waves may contribute towards SIBO. (I also believe that a weak Ileocecal valve may contribute towards SIBO by allowing reverse entry of microbes from the Cecum into the Ileum. Weakness of the Ileocecal valve may be due to Straining during evacuation)
          An overgrowth of Methane producing Archae microbes in the Colon (they consume Hydrogen produced by other Commensal Microbes) are thought to contribute towards Chronic or functional Constipation by impacting on Gut Motility via the neurotrnansmitter Serotonin. Modulating the population of these microbes or inhibiting the process of Methanogenesis may help to normalise Gut motility. There is a belief that some people are Methane producers and others are either non producers or Hydrogen producers. I do not think it is as clear cut as that. Perhaps some people produce less Methane due to the composition of the microflora in the Gut.

          Methane on breath testing is associated with constipation: a systematic review and meta-analysis.
          Methanogens in Human Health and Disease
          Methane and the Gastrointestinal Tract
          Methanogens, Methane and Gastrointestinal

          One of the ingredients in TRIPHALA is Terminalia Chebula. This herb has been found to inhibit methanogenesis and reduce the production of Methane Gas and so contribute towards Gut motility.


          Inhibition of methanogenesis by human bile

          Inhibition of Methanogenesis :
          useful Herbs are:
          1. Terminalia Chebula ( one of three ingredients in the Ayurvedic formulation “TRIPHALA”)
          2. Indian Gooseberry, more commonly known as “Amla”…..Emblica Officinails (the second ingredient in “TRIPHALA”)
          3.Garlic, Garlic Powder, Garlic oil
          1. Ginger
          2. Turmeric (may work via anti-microbial action or indirectly by inducing Bile secretion from Gall Bladder)
          3. Cloves
          4. Nutmeg
          5. Thyme and Ajwain (both contain Thymol and Carvacrol)
          6. Fatty foods and oils may work by inducing secretion of Bile, which has anti-microbial properties.
          Some of the spices are found in spice Blends used daily in Indian households.
          1. Curry Powder (Turmeric, Dried Ginger, Cumin, Coriander, Mustard Seeds, Cayenne (Chilli)Powder
          2. Garam Masala ( Cloves, Nutmeg, Cardamom, Black Peppercorns, Cumin, Cinnamon)
          3. Tea Masala (also known as Chai Masala) (Peppercorns, Dried Ginger, Cardamom, Cinnamon, Cloves, Nutmeg and some people add Fennel)
          It is quite possible that it is the balance between Hydrogen and Methane gas produced that determines the final result on gut motility. Some of the above Herbs/spices are known to inhibit methanogenesis while others are thought to increase Hydrogen via fermentation by suitable commensal microbes.