The SIBO Saga: Part 3

sibo3Disclaimer:  As I have said in the past, I’m not a research blogger.  I’m here to mix “data with soul” and give you useful info, but only in the context of my real, human experience.  That is not to say that citation on my part and proper follow-up on your part are not important.  Everything I wrote about in this blog was presented by Dr. Steven Sandberg Lewis, ND & Dr. Allison Siebecker, ND at the SIBO Symposium during January 2014 and you can pay to have access to those presentations through the National College of Natural Medicine’s website.

Here we go again, another SIBO blog this week.  We’ll be chatting about herbal antibiotics and a few pieces of miscellaneous SIBO “stuff” that I thought should be shared.  This topic is not getting old for me (and I hope not for you, either).  The more I learn, the more I see how easily people, especially those of us dealing with autoimmune diseases, can find themselves in the grips of SIBO and how it can be missed by our doctors for years if a patient doesn’t have the details to advocate for his or her self.

At the Symposium, Dr. Steven Sandberg-Lewis, ND gave the talk on herbal “antibiotics.”  These are herbs, extracts of herbs, or combinations of herbs that are powerful enough to slow the growth of or kill micororganisms.  He started his talk by identifying the most commonly overgrown organisms in a SIBO infection, something I wanted to write about, because it is very useful if you prefer that your doctor treat SIBO with herbal antibiotics, since certain herbs are more effective against certain organisms than others.

Most to Least Common Anaerobic (do not require oxygen) Bacteria in SIBO

  • Bacteroides
  • Lactobacillus
  • Clostridium
  • Aeromonas

Most to Least Common Aerobic (needs oxygen) Bacteria in SIBO

  • Streptococcus
  • E. Coli
  • Enterococcus spp
  • Staphylococcus
  • Klebsiella
  • Proteus mirabilis

There are some reasons you may want to choose herbal antibiotics.  First, they are biodegradable and do not end up in our water supply, as regular antibiotics do.  The possibility that bacteria will become resistant to them is much lower, since there are hundreds of compounds found in a single herb.  They often have other effects, such as being anti-inflammatory, anti-fungal, and anti-viral.  Extracts of herbs can also allow for significantly increased potency, which is usually not safe with regular antibiotics.  A draw back to choosing this treatment path, is that while antibiotics can work within two weeks, the herbal course may take four to six weeks.

The first group of herbs Dr. Sandberg-Lewis spoke about are the Berberine herbs.  They all have the plant alkaloid, Berberine in common, which is antibiotic, along with many other healing effects.  Sandberg-Lewis focuses on using Goldenthread, Goldenseal, Huang Bo, Oregon Grape, and Barberry to treat his SIBO patients.  Normally, he uses capsules containing two or three of these herbs, so that patients can take several at a time, since the dose may need to be as much as 5000 mg/day for a difficult overgrowth.  Berberine is most effective against Hydrogen-Dominant SIBO or SIBO with diarrhea.

I found this interesting, since my experience using herbal antibiotics was with a treatment that used many of the above named Berberine herbs, along with several anti-parasitic herbs, but the recommended dose was not nearly high enough, which may be one reason the herbal course did not work for me.  Another reason it did not work, was that I did not tolerate it well.  We often have the mistaken idea that herbs will be more gentle for the body, but that is not necessarily the case.  One possible reason for my intolerance . . . Berberine herbs can lower blood glucose levels.  This is a potentially positive effect for a diabetic, but for me it was awful.  Dr. Sandberg-Lewis noted that patients will start the herbal course and then complain about the effects of die-off, when in reality they are experiencing low blood sugar episodes.  Now that I understand this, I am almost certain my intolerance to the herbal course had alot to do with low blood sugar.  Berberine herbs can also have an effect on SSRI (anti-depressant) medications, so it could be important to keep that in mind if you are treating depression while dealing with SIBO.

The next herbal treatment Dr. Sandberg-Lewis spoke about was garlic or the more potent garlic extract, Allicin.  Garlic is a high FODMAP, so some of you that know those with SIBO should be avoiding high FODMAP foods are probably wondering why it is used as an herbal antibiotic.  The extract, Allicin, is fructan (the sugar named with the F in FODMAP) free, so not an issue for patients who need to use it.  Garlic needs to be combined with the berberine herbs to treat Methane-Dominant SIBO or SIBO with constipation.  Garlic is also anti-fungal, which can be useful for those who are prone to yeast overgrowth.  One word of caution, is that Garlic can prolong bleeding time, so those on blood thinners should be aware of the interaction.

Finally, Dr. Sandberg-Lewis talked about his use of Neem and Oregano Oil in treating SIBO.  He stated that he almost always uses Neem with the Berberine and/or Garlic, because he feels it enhances the potency of the other herbs.  It is also highly anti-inflammatory, anti-viral, and can be anti-ulcer.  He uses Oregano Oil less often, but does find it useful.  His reason for using it less often is patient intolerance.  This also confirms my experience using it to treat SIBO.  Oregano Oil is very powerful and left me feeling quite rough.

Dr. Sandberg-Lewis also talked about natural factors that can help in the treatment of SIBO.  He pointed out that any deficiencies in stomach acid, pancreatic enzymes, and bile should be addressed.  Again, this confirms my experience, since identifying pancreatic enzyme deficiency and treating it, was a factor in helping me not only deal with SIBO, but other health concerns I had early in my Celiac diagnosis.  Also, having intacted anatomy and motility of the GI system plays a role.  The migrating motor complex must be working properly, the ileocecal valve must be working properly (this valve keeps the contents of the colon out of the small intestine), and the microvilli of the small intestine must be healthy.  Since damage is to the microvilli in Celiacs, this may be one reason we are so susceptible to SIBO.

Dr. Sandberg-Lewis also touched on the idea that SIBO may be incurable in some cases.  He found this with patients that have had continuous, long-term use of proton-pump inhibitors (PPIs, like Nexium), because it disrupts stomach acid production so much.  He found this with patients who had continuous use of opiate painkillers, because it disrupts migrating motor complex.  He also noticed it with patients that had altered anatomy or motility (so surgeries that changed the GI tract or anything that changed GI movement).

Dr. Sandberg-Lewis and Dr. Siebecker also did a presentation where they spoke about key indicators that SIBO could be at play.  I found this really interesting and recognized myself in the list.  If you find yourself in one of these positions, it is worth asking your doctor to take a deeper look, for possible SIBO.

  • Low ferritin levels that are not explained by anything else, this may be malabsorption caused by SIBO
  • Noticing alleviation of GI symptoms after antibiotic treatment for an unrelated issue
  • GI symptoms getting worse after probiotic use (being one of those people who says, “All probiotics make me feel worse.”), as it may be the prebiotics in the probiotic feeding the SIBO
  • If eating more fiber INCREASES constipation
  • GI symptoms developing after a short-course of opiate use (decreases migrating motor complex & may let SIBO take hold)
  • GI symptoms developing after proton-pump inhibitor use (stomach acid is not strong enough to kill bacteria & may let SIBO take hold)
  • Diagnosed Celiac that is not improving, despite strict gluten free diet (I definitely had this issue & probably should have been treated for SIBO much earlier)

Okay, that’s a long entry in the SIBO saga today, but I think all good information!  I will be writing about Diet for SIBO and also other health issues that are connected with SIBO in the coming weeks, so stay tuned.  Sooo much to cover!

You can find Part 4 of the SIBO series here.

About Angie Alt

Angie Alt is a co-founder here at Autoimmune Wellness. She helps others take charge of their health the same way she took charge of her own after suffering with celiac disease, endometriosis, and lichen sclerosis; one nutritious step at a time. Her special focus is on mixing “data with soul” by looking at the honest heart of the autoimmune journey (which sometimes includes curse words). She is a Certified Health Coach through the Institute for Integrative Nutrition, Nutritional Therapy Consultant through The Nutritional Therapy Association and author of The Alternative Autoimmune Cookbook: Eating for All Phases of the Paleo Autoimmune Protocol and The Autoimmune Wellness Handbook. You can also find her on Instagram.


  • […] SIBO Saga:  Part 3 can now be found HERE, at Autoimmune Paleo, where I and my blog partner, Mickey Trescott, now blog.  Thanks for […]

  • […] You can find Part 3 of the SIBO series here. […]

  • […] because it seems as though there are circumstances in which SIBO can be untreatable, one of them being historic daily use of opiate painkillers. Something Matthew has done over the […]

  • Mela says

    Do you have any advice for GERD, the kind that feels like something is stuck in your esophagus? I am going on my 3rd day of only being able to drink water. Even broth will not go down, nothing. If I try it gets stuck immediately above the diaphragm and there is pressure and burning there. I have been drinking Gerolsteiner Mineral Water because the natural bubbling enables me to burp sometimes and that helps release the pressure. After 8 hours of sleep I feel good but I cannot take anything but water without activating the GERD.
    I have bee diagnosed with SIBO and citrobacter (in lower intestine) and have been treating the SIBO 4 weeks with oregano oil. The consistency of my elimination is greatly improved and as of this morning still is. I was doing well eating meat and vegetables and bone broth, until I had a drink of alcohol, to celebrate(?), and since then I have been in this GERD state. I am wondering how long I can last on water only.

  • […] herbs … all have the plant alkaloid, Berberine in common, which is antibiotic, along with many other healing effects. Sandberg-Lewis focuses on using Goldenthread, Goldenseal, […]

  • Afshin says

    Hi . Can I take appel vinegar before eat because of my low acid . And I can take herb as well ?

    • Angie Alt says

      I’m sorry, but since I am not a doctor or naturopath and don’t know your history, I can’t advise you specifically on either of these.

  • Holli Nesbitt says

    Thank you for your article. Its very interesting to me. I have celiac that wont heal on a gf diet. Went to a functional medicine nutritionist and have been diagnosed with sibo a few months ago. Ive been geeting visceral manipulation therapy every 6 weeks for mmc and keep my valve in check and also did the elemental diet. After elemental i felt great for a couple weeks then my sypmtoms started to creep back up so i started fc cidal dysbiocide and oregano i felt better for 3 weeks and the last week of them i started feeling bloated again. We just switched to allimed berberine and still fccidal. All along ive followed a lowfod maps and have also been taking ginger to stimulate mmc as well as hcl for stomach acid production. My enzyme levels of amalase and lipase are actually great levels without having to take enzymes. I tried bile and it aggrivated my right side where my gallbladder used to be BIG time so we did stop that. Im afraid to try it again. We are suspecting i may have small intestinal fungal overgrowth now with a little sibo…as it mimics the same symptoms. I did a candida spit test and it showed tenticals hanging down from my spit. I feel so frustrated bc as the days go on my bloat becomes more intense. I feel myself slipping back to how i felt before elemental. I know herbs take a long time but my question is…..are my bloat symptoms die off or my herbs not working? The fact that i was felling better and gradually getting more bloat seems like im not winning the fight here but i dont really know what die off is supposed to feel like? I follow lowfod maps but i do eat low fod map fruits..a few servings a day. If i could be dealing with fungal overgrowth as well as sibo woukd eating fruit be bad? I dont eat any honey sugar or any juice ..nothing else sweet. Just grapes oranges pineapple and strawberries.

    • Angie Alt says

      Hi Holli! Very sorry to hear about your long journey w/ Celiac & SIBO. I wish I could give you more specific feedback, but I’m not a medical practitioner, so I can’t tell you if your symptoms are die off or the herbs not working. It does sound like you are getting closer to figuring it out w/ all the steps you are taking though. Best of luck!

      • Holli Nesbitt says

        Thank you! From your celuac sibo journey how long did it take to heal your gut and what protocol of herbs did u use?

        • Angie Alt says

          It took me about 3 attempts over the course of probably 1-2 years total (w/ some long periods of no symptoms). I did not stay on the herbal protocol for long, because it did not agree w/ my body and it was a blend of many different herbal “antibiotics.”

          • Holli Nesbitt says

            When you finally got rid of your sibo is that when your celiac healed as well?

  • Heidi says

    Can you tell me more about the exact symptoms you experienced when you say the Oregano Oil left you feeling rough? Or specifically what it felt like to be intolerant to the herbal supplements?

    • Angie Alt says

      Basically, it felt like getting sick. Very painful headache, achey, tired, upset stomach, etc. Some will say this is “die-off,” but I don’t think those uncomfortable symptoms should be allowed to continue unchecked for longer than 3 days. Hope that helps!

      • Heidi says

        Thanks, Angie. Did you deal with any brain fog along with the other un-fun symptoms?

  • Sandy Newman says

    Fantastic article, thank you! So helpful. But quick ? What if you have a combination SIBO of Hydrogen & Methane dominant alternating between diarrhea and constipation:

    Do you do both Berberine & Allicin at the same time? Or do one and then the other?

    Thank you!


  • Lkn says

    Can you give any advice for someone who can’t take the berberine herbs? They interact with my medication so I can’t take them at high doses. Would anything else work?

    • Angie Alt says

      Hi Lkn-
      I can’t recommend herbs or medications, as I am not a medical doctor & don’t know your case. I would look at Dr. Alison Siebecker’s site for some guidance on other herbal SIBO treatment options.

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