Episode 29: SIBO with Dr. Melanie Keller

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What Is Small Intestine Bacterial Overgrowth (SIBO)?

SIBO stands for Small Intestine Bacteria Overgrowth. Having bacteria in our bodies is a normal state of being. In fact, 90% of our body is made up of microbes. So what’s the problem with finding them in the small intestine? Well, they don’t belong there, at least not in high numbers. Whereas the large intestine is the natural home for billions of microbes, a healthy small intestine only has about 100,000. So, basically, they’ve migrated. Have you ever dealt with invasive plants in your yard? They tend to take over and cause all sorts of problems. The same thing happens in the small intestine. In today’s podcast, we’ll discuss why this happens, how it relates to autoimmune disease, and the most effective tests and treatments. Our guest, Dr. Melanie Keller, has battled SIBO herself and now specializes in its treatment professionally.

Listen to the Show

Show Notes

  • Intro (0:00)
  • Meet Melanie (0:51)
  • Thank You to our Podcast Sponsor – Paleo on the Go (2:07)
    • A frozen meal delivery service, they have a large menu of items for the paleo autoimmune protocol (AIP).
    • Use the code PHOENIX for 10% off your first order.
  • Melanie’s Personal Healing Story (3:11)
    • She was treated with multiple antibiotics for chronic ear infections as a child, which is a risk factor for developing SIBO. She experienced constipation from a very early age, never knowing that wasn’t “normal.” Back then, gastrointestinal issues were believed to have psychological origins, so she was prescribed anti-depressants, which did nothing to improve her condition. It wasn’t until she was in naturopathic school and started to look into diet and lifestyle, that she saw the connection between the food she ate and how she felt. SIBO research was also emerging at that time, particularly the book Functional Gastroenterology by Steven Sandberg-Lewis. That information eventually led to her diagnosis and treatment.
    • She followed a grain-free, low-FODMAP diet for a long time, but has reintroduced gluten-free oatmeal and white rice in small amounts and finds that optimal for her digestion and energy levels. As she has healed, she’s also been able to reintroduce FODMAPs in small quantities, but she’s careful not to eat too many in one sitting. Healing the microbiome is a dance that requires tuning into your body, taking small steps forward, and adjusting as needed.
  • The Connection Between SIBO and Autoimmune Disease (10:27)
    • There’s a lot of interaction between the gut microbiome and the immune system, and there is emerging research that certain types of microbes, or simply an imbalance in microbes, can trigger autoimmune disease.
    • Autoimmune disease itself is also a risk factor for SIBO. So it can be a vicious cycle of autoimmune disease causing SIBO which then amplifies the autoimmune expression.
  • The Connection Between SIBO and Other Health Conditions (12:36)
    • SIBO is involved in many other health conditions. Here’s a complete list. Rosacea, in particular, is often dramatically improved after SIBO treatment. (See these before and after photos.)
    • Moderate alcohol consumption can worsen or even cause SIBO.
    • Dr. Keller believes that in 10 years, a SIBO breath test will be part of every routine physical.
  • What are the Classic Symptoms of SIBO? (15:40)
    • Abdominal bloating: “I just want to unzip my belly.”
    • Variable stools: either hard and soft stool in one bowel movement, or alternating between constipation and diarrhea.
    • It’s also common to have a short healing crisis at the start of SIBO treatment where symptoms get worse for a few days before they get better.
  • SIBO Testing and Diagnosis (18:20)
    • Pubmed will list the “gold standard” for testing as an endoscopic aspirate. But it’s expensive, invasive, painful, and often inaccurate because it doesn’t reach the entire small intestine.
    • The test used and recommended by most specialists in the field, including Dr. Pimentel and Dr. Keller, is the Lactulose Breath Test. It measures for two gases: methane and hydrogen, which are produced by the bacteria throughout the small intestine.
  • Bacteria in the Small Intestine vs. the Large Intestine (21:36)
    • SIBO isn’t an overgrowth of pathogenic bacteria. Rather, it’s a condition where there is an overgrowth of normal bacteria in the wrong place. The large intestine is the natural home for billions of microbes, whereas a healthy small intestine only has about 100,000. SIBO occurs when there are too many bacteria in the small intestine.
    • SIBO cases range in severity. Some people respond to treatment quickly. Others have more complex issues that require longer treatment protocols.
  • Prokinetics and the Migrating Motor Complex (22:05)
    • The Migrating Motor Complex (MMC) is designed to prevent SIBO from happening. It’s a cleansing wave through the small intestine that ideally occurs 11 times daily. Many people with SIBO only get this wave 3 times daily.
    • Prokinetics are either pharmaceuticals or herbal supplements that stimulate the MMC to produce cleansing waves more frequently. They are the second phase of SIBO treatment, added after the bacterial overgrowth has been eliminated. They help prevent SIBO recurrence.
    • For prokinetics, Dr. Keller recommends either the pharmaceutical: low-dose Erythromycin or the herbal supplement: ginger with 5% gingerols.
    • Some people only need to take prokinetics for a few months, while others need them for years. The people who need them long-term usually have autoimmune activity targeted on the MMC that was caused by a food poisoning event in the past. There’s a specific test for this autoimmune activity called IBSchek.
  • Dietary Treatment for SIBO (34:09)
    • There are a variety of diets recommended as part of the treatment plan for SIBO, and different ones are chosen based on physician preference and patient needs. What they all have in common is that they limit carbohydrates that are known to be food for bacteria, thereby starving out/preventing overgrowths. Here are links to more information on each one: SCD, GAPS, Low-FODMAP, SIBO Specific Diet, Cedars-Sinai Diet, and Elemental Diet.
    • SIBO cannot be treated with diet alone. While diets can minimize your symptoms and make you feel better if you have a mild case, you cannot eradicate SIBO without some antibiotic intervention (either pharmaceutical or herbal).
    • During antibiotic treatment, you want to be sure you aren’t too strict with your diet. Starved bacteria hide under biofilms and antibiotics can’t reach them. Rather than taking an anti-biofilm agent, Dr. Keller recommends you feed them just enough to keep them out in the open, so the antibiotics will be more effective. She recommends 2-4 servings of white rice if tolerated, or other fermentable carbohydrates like a small amount of FODMAPs: avocado, broccoli, onion or garlic.
    • SIBO diets are often followed for a few months after treatment to help a healthy microbiome re-establish and prevent SIBO recurrance. But these aren’t meant to be permanent diets – so work with your practitioner to slowly expand your diet again. Meal plan resources for this short-term dietary intervention: 28 Days of Low-FODMAP AIP and FODMAP-Free Paleo Breakthrough.
  • Herbal Antibiotics for SIBO (37:10)
    • Antibiotics are necessary to successfully treat SIBO. Dr. Keller uses two herbal antibiotics, which she finds to be just as effective (if not more so) than pharmaceuticals: Allimed and Neem Plus. Usually she sees profound results in just two weeks. She said that pharmaceutical antibiotics can also work, but in chronic cases, they don’t work as quickly as the herbs.
  • Probiotics and SIBO (48:14)
    • Dr. Keller takes people off all probiotics during treatment and for a minimum of 3 months afterward. This includes fermented foods as well as supplements. She believes it takes that long for the immune system to “reboot” and it’s best not to interfere during that process. Probiotics are immune stimulants, and they can push the immune system the wrong way. When probiotics are reintroduced too soon, bloating is usually the first symptom to return.
    • Dr. Keller actually never recommends the reintroduction of probiotic supplements. When the time is right, she would rather reintroduce probiotics naturally through small amounts of fermented foods, and the careful reintroduction of fermentable foods that naturally increase probiotics in our gut, like green plantains and sweet potatoes and other prebiotic foods.
  • Bone Broth and SIBO (53:25)
    • Bone broth is a healing food recommended in the paleo autoimmune community, because it helps nourish the body at a cellular level. However, if you have an active case of SIBO, bone broth isn’t your friend. This is because the cartilage in bones breaks down into food for bacteria. A SIBO-safe alternative is broth made from meat only (no bones) and cooked for a shorter period of time (4-5 hours).
    • After successfully treating SIBO and waiting 3 months for your immune system to “reboot” you can try slowly reintroducing small amounts of bone broth again.
    • If you haven’t been tested for SIBO but find that you experience bloating after drinking bone broth, that’s an indication that you should be tested.
  • Stress and SIBO (56:56)
    • Stress management is an essential part of a SIBO healing protocol.
    • One of Dr. Keller’s favorite techniques is Free Writing: Set a timer for 20 minutes. Get a pencil and paper, because you need to physically write. And then just let it all out – uncensored – whatever you’re feeling. Afterward, destroy the paper. Then, go for a walk if you can, because the alternating movements of the arms and legs helps decompress from that release.
    • Another technique Dr. Keller likes is Emotional Freedom Technique (EFT).
  • What Constitutes Cure? (1:01:18)
    • It depends on the severity of the SIBO. Some cases are simple, easy to treat, and people feel 100% better. Others have struggled with SIBO for years before finding a practitioner like Dr. Keller to help them. In those cases 75% improvement is very possible and can feel like a miracle..
  • Outro (1:02:17)
    • Dr. Keller works with patients around the world via Skype and will soon also have in-person office hours in both Portland and Los Angeles. Her website is SIBO Solution.
    • Eileen (your podcast host) is the author of multiple books, written to help people thrive with autoimmune disease. Learn more on the Books Page.
    • If you like this podcast, follow or subscribe through your favorite podcast app. You can also subscribe to Eileen’s biweekly newsletter.
    • Check out the entire archive of podcast episodes.

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25 comments on “Episode 29: SIBO with Dr. Melanie Keller”

  1. Thank you Dr Keller and Eileen for the great podcast. I have been seeing a nutionist for what we think is sibo for month. I asked my functional MD for the breath test as I have been strictly on SCD for 90 days, I just finished rounds of herbal antibodies. I am not happy with the MD and think the well meaning nutritionist has done just what may not been helpful. I am thinking of going to Dr Keller but do not have a true diagnostic yet, I have the breathe test sitting here, I just finished 10 days ago the herbals and probiotics. Would that prevent a true reading, ?? Jackie

  2. Hi Eileen,

    I have Hashimoto’s and I think I gave myself a case of SIBO by taking too strong of probiotics. I thought I might have been making that up in my mind trying to find a connection…so happy she mentioned that. I am curious about the length of time to stay on the herbal “antibiotics”. She says she sees results many times in 2 weeks…do you stay on just for the 2 weeks if you do get results…or do you need to stay on longer past that time frame.

    Thanks for all you do!


    1. Hi Latifa. You really need to be tested for SIBO rather than trying to self-diagnose and self-treat. Treatment depends on test results, and there is a wide variety of results that lead to different prescription recommendations. It’s also quite possible you don’t have SIBO at all. Dr. Keller works with people worldwide via Skype. Alternatively, you can look for other paleo practitioners through these directories. Functional medicine practitioners (including Dr. Keller) offer SIBO testing as well as other effective tests to help troubleshoot health issues.

  3. Wonderful podcast, thank you so much. I have been suffering with SIBO, rosacea and other related issues for over a decade. I have taken Rifaximin twice and tried all the diets. My blood work does not show autoimmune disease but I’m not so sure. The AIP diet with low FODMAPS (I’ve done both alone with limited success) looks very promising to me. Question: if bone broth is bad for SIBO, is hydrolysate collegen okay? It could serve some of the same gut healing and skin supporting purposes of bone broth. Please respond, I have searched and searched and cannot find an answer to this. Thank you for your important work!

    1. Mira, I don’t know the answer to that question. You can set up a consult with Dr. Keller and ask her, though. In the meantime, just follow her suggestion to make meat broth instead of bone broth. The recipe link is in the show notes above.

  4. I’m part of a Facebook group on AIP in the UK and a member referred me to this podcast. I’m so thankful. I’ve been convinced that I’ve responded not just neutrally to probiotics but actually had an unhappy response to them– and it is helpful to hear Dr Keller’s take on this. The whole interview was enlightening, especially about feeding the lower gut bacteria during treatment with some fodmap/starch! This area of research is cutting edge and I truly hope that the number of controlled studies and refereed papers can grow.

    1. Yes, I think the research will continue to grow in this area. It’s interesting about the probiotics, because once upon a time, they were recommended by all functional medicine practitioners. Now, the advice seems to be split 50/50 – some still swear by them and others like Melanie warn against them. Like you, I’ve had negative reactions, so I tend to side with Melanie.

  5. If a person has a leaky gut and SIBO which do you treat first? The diets are different enough to cause problems for both.

      1. Thank you for the reply. Apparently the functional medicine dr I’m seeing is not doing this right. Do you have a link to this information that I can pass on to him?

        1. HI Susan. I recommend sharing this SIBO podcast with him and also the interview with Dr. Alessio Fasano (leaky gut expert) who mentions SIBO as a cause of leaky gut. However, you might just want to work with Dr. Keller (the SIBO expert in this interview) if you aren’t confident in your current functional dr. Wishing you wellness!

  6. Maybe I should have put the pieces together that probiotics are immune supporting, but I really didn’t. I’m surprised because even Sarah Ballantyne’s book has suggestions about which kind to take and she has mentioned on podcasts and her website that she takes Prescript-Assist. I didn’t do any research myself, but went online and bought that one. I didn’t find it really relieved any of my digestive symptoms anyway, but I wish I had known about this sooner. I take injections for MS that modulate my immune system. I shouldn’t be taking anything that will mess that. Thanks for AGAIN sharing such important information! You’re truly the best resource I have found!

    1. You’re welcome, Corianna. It’s interesting, because probiotics have universally been recommended for a long time, but that is starting to change. In the interim, advice is mixed. I tend to side with Dr. Keller, because I personally have never experienced a benefit from them. I prefer fermented foods and see them as both more diverse and more natural. I also think Dr. Fasano made a good point in Episode 32 of this podcast, that our microbiome needs are too unique to all be treated with the same probiotic.

  7. All the pieces of the puzzle are finally coming together! I love and look forward to all of your podcasts! I find them so professional with questions that get straight to the point and give us a clear and complete synopsis of the subject. Thank you so much for all that you do and know that it makes a huge difference to me and I’m sure many others.

  8. I am still confused about the recommendation of not taking probiotics. It seems like every practitioner I have seen, have recommended. The only time, it wasn’t recommended was if I had signs that I needed to repair the lining of my gut. I am sure there are exceptions to the rule (ex. since if someone has sibo, in addition to dysbiosis/yeast overgrowth then probiotics may be essential to the healing process). Thoughts?

    1. Angeles, did you listen to the podcast? She explained her reasoning quite clearly. Since probiotics stimulate the immune system, she has seen them do more harm than good in many of her patients healing from SIBO and autoimmune disease. While you are right that probiotics have been recommended by many practitioners for a long time, the tide seems to be turning. Fermented foods continue to be recommended, but more and more people are becoming cautious about the overuse of probiotics. This came up in my recent interview with Dr. Alessio Fasano this week as well.

  9. That “90% of our bodies” statement had me wondering, do you mean 90% of the CELLS in our bodies? That’s the only way I can imagine that to be true since bacteria are so much smaller than our cells. I know you didn’t mean to suggest 90% by volume or 90% by weight, two other ways to read that.

    Thanks for this. It’s a topic near and dear.

    It may interest you to know that SIBO is a regular occurrence for many who deal with scleroderma. Decreased GI motility with the disease creates a conducive environment. Decreased motility also increases esophageal reflux. Unfortunately, the standard medical response to reflux is a PPI to reduce stomach acid, which *further* delays stomach emptying by prolonging digestion. I did try a PPI (and felt horrible); but I learned I was able to manage my reflux by increasing bowel throughput by increasing the fruits and vegetables in my diet.

    Thanks so much for all you do for our AIP community.

    1. Hi Meghan – yes microbes comprise 90% of our cells and 99% of our genetic material! It’s amazing to consider. Thank you so much for the information on the connection between SIBO and scleroderma. It makes sense, and I can see where it could be the missing key element in some people’s healing strategy.

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