STOP IBS With This Natural SIBO Protocol

STOP IBS With This Natural SIBO Protocol

It’s a safe guess you’re here because you have gas, bloating, constipation, diarrhea, stomach pain or a combo. If it’s been bothering you for months or years, a doctor may have diagnosed you as having Irritable Bowel Syndrome (IBS) and advised that you learn to live with it. But what if you can be free from IBS?

IBS symptoms usually indicate a microbial imbalance in your small intestine. To give you a sense of scale, there are over 500 species of bacteria in your gut with a combined gene count that outnumbers your own 100:1.

Dr. Mark Hyman explains, Among all that gut bacteria, there are good guys, bad guys, and VERY bad guys. If the bad guys are allowed to take over, or if they move into areas that they shouldn’t be (like the small intestine which is normally sterile), they can start fermenting the food you digest, particularly sugary or starchy foods. This produces an imbalance in your gut ecosystem that can trigger or exacerbate irritable bowel syndrome – including leaky gut, small intestinal bacterial overgrowth (SIBO), and yeast overgrowth.”

According to a Dartmouth-Hitchcock Medical Center study, up to 80% of people with IBS have SIBO. If you’re struggling with IBS, here’s hope. You may be able to STOP IBS with this natural SIBO protocol or a non-absorbed pharmaceutical antibiotic.

IBS indicates a microbial imbalance in your small intestine. Here's how to STOP IBS. Click To Tweet

Before we get into the details, let’s meet the doctors we’re learning from.

Introducing our SIBO specialists!

I chose these particular doctors because they are on the forefront of SIBO discoveries and breakthroughs. Their research is informing the entire medical world on SIBO and IBS.

Dr. Mark Pimentel, M.D.

Dr. Pimentel is referred to more than any other expert I encountered. He works at the Cedar Sinai medical complex in Los Angeles, California. He is Program Director for the Medically Associated Science and Technology (MAST) Program, an Associate Professor of Medicine and an Associate Professor of Gastroenterology.

Dr. Pimentel has made some impressive scientific discoveries.

  • Discovered that IBS is a condition of altered intestinal microbial balance.
  • Discovered that methane-producing bacteria in the gut can cause constipation.
  • Found that pathogenic bacteria impact the intestine via a molecular mimicry mechanism.

He is also the author of: A New IBS Solution: Bacteria-The Missing Link in Treating Irritable Bowel Syndrome.

Dr. Allison Siebecker, ND, MSOM, LAc

Often called the SIBO Queen, Dr. Siebecker has has specialized in the treatment of SIBO since 2010. She’s tearing it up making information available online and I’ve quoted her more than any other. Some of her qualifications:

  • Co-founder and former medical director of the SIBO Center for Digestive Health at the National University of Natural Medicine (NUNM) Clinic
  • Instructor of Advanced Gastroenterology at NUNM
  • IBS Board of Advisors
  • Faculty for the GI Health Foundation
  • Co-Founder & Curriculum Coordinator of the 2014-2016 SIBO Symposiums
  • Teaches continuing education classes for physicians
  • Author of the free educational website
  • Currently writing a book synthesizing SIBO data into one source

Dr. Michael Ruscio, DC

Dr. Ruscio hosts an excellent podcast called Dr. Ruscio Radio. He also specializes in treating gut dysbiosis (microbial imbalance). His background:

  • Functional Medicine Practitioner
  • Lead researcher in current IBS study
  • Post-doctoral continuing education provider
  • Doctor of Chiropractic – Life Chiropractic College West
  • University of Massachusetts – B.S. Exercise Kinesiology
  • Post-doctoral Functional Medicine study with educational bodies such as; The National College of Naturopathic Medicine, The Institute of Functional Medicine, The American Academy of Anti-Aging Medicine, Kalish Research, and Defeat Autism Now.

There are many other functional medicine practitioners knocking it out of the park with SIBO. I’ll introduce a few of them along the way also.

How you can you tell if you have SIBO? There are textbook symptoms.

SIBO symptoms

You can take a quiz here to find out how likely SIBO is for you.

Common symptoms of SIBO include:

  • Abdominal pain and cramps
  • Anxiety induced insomnia
  • Belching
  • Bloating – a.k.a. a “food baby”
  • Constipation
  • Diarrhea
  • Fatigue
  • Flatulence / Gas
  • Histamine intolerance
  • IBS
  • Malnutrition
  • Nausea
  • Restless leg at night
  • Vomiting
  • Weight loss
Bloating, constipation, gas and diarrhea are symptoms of SIBO. Click To Tweet

IBS predisposes SIBO

Irritable Bowel Syndrome (IBS) is a label to describe when these symptoms have persisted for months. Dr. Ken Brown calls IBS a “trashcan diagnosis“. It often means, “We don’t really know what to do next.”

It isn’t technically accurate to say SIBO causes IBS. Rather, you could say IBS predisposes SIBO. If you have IBS, there’s a high probability you have SIBO.

Here are some insights from newer studies.

  • IBS affects 11-14% of the population.
  • 92% of IBS patients share the symptom of bloating.
  • 84% of IBS patients will have an abnormal lactulose breath test. This is the main test used to detect SIBO.
  • IBS symptoms improve 75% after eradication of SIBO.
  • IBS “is a puzzling condition with multiple models of pathophysiology including altered motility, visceral hypersensitivity, abnormal brain-gut interaction, autonomic dysfunction, and immune activation.”

Other diseases predispose SIBO also.

  • 75% of patients with diabetes tested positive for SIBO.
  • 66% of celiac patients with persistent symptoms, despite adherence to a strict gluten-free diet, tested positive for SIBO. “All of these patients noted a resolution of their symptoms after being treated for bacterial overgrowth.”
IBS symptoms improve 75% after eradication of SIBO. Click To Tweet

So what’s the SIBO and IBS connection? In a word, gas.

Bacteria produce gas. Gas correlates to IBS symptoms.

Did you know humans don’t produce gas? 500 species of bacteria in your gut do. They eat your food and then excrete hydrogen gas (H2).

Hydrogen feeds another kind of microbe called archaea, which are technically not a bacteria. Archaea are tough little critters. Some can even thrive in deep sea volcanic vents or in pH the same as battery acid, according to NASA.

There are different kinds of archaea, including groupings called methanogens, acetogens, and sulfate-reducing bacteria (SRB).These organisms produce methane (odorless gas), acetate (can dismutate to methane and carbon dioxide), and hydrogen sulfide (H2S -flammable and smells like rotten eggs), respectively.

Dr. Siebecker says, “The gas causes abdominal bloating, abdominal pain, constipation, diarrhea or both (the symptoms of IBS).  Excess gas can also cause belching and flatulence.”

Hydrogen has a greater association with diarrhea. Methane has an exclusive association with constipation. This is why you sometimes see letters after IBS. There’s IBS-D (Diarrhea), IBS-C (Constipation) and IBS-A (Alternating).

I’m using words like “associated” and “correlates” because scientists have not yet pinpointed exactly why methane is so closely tied to constipation. They just know symptoms track closely with the amount of methane measured.

In addition to gas, diarrhea and constipation, Dr. Siebecker points out how bacteria can be responsible for other problems.

  • Some of their favorite nutrients to eat are iron and B12. Over time, they can make you deficient, which can result in anemia.
  • They deconjugate bile, which leads to a deficiency in vitamins A & D. You may also notice fatty stools.
  • Hydrogen sulfide is thought to promote hyperpermeability (leaky gut) by harming the mucosal lining of the small intestine.
  • Leaky gut allows undigested proteins and even bacteria themselves into the blood, which activates the immune system. This causes food allergies and sensitivities and can lead to autoimmune conditions.
  • Bacteria also excrete acids, which can cause neurological and cognitive symptoms in high amounts.
Bacteria produce gas. Gas correlates to IBS symptoms. Click To Tweet

SIBO causes and risk factors

SIBO Causes:

SIBO Risk Factors:

Of all the risk factors, food poisoning appears to be the most prevalent.

Dr. Pimentel: “…we think food poisoning causes some kind of neuropathy or motility disturbance of the intestinal tract, and then you get stasis or slowing, and then the bacteria start to accumulate.  I would say that probably 70% or 80% of patients who come to me with overgrowth, that’s the mechanism of action, or at least that’s what we feel is the mechanism, and that it’s a reduction in the migrating motor complexes as a result of some insult in the past.”

Dr. Pimintel thinks it works like this:

Food poisoning -> CdtB toxin becomes elevated in the blood -> nerve cells are damaged -> impaired motility -> Bacteria proliferation -> SIBO

Most IBS begins with deficiency of the Migrating Motor Complex. Here's how it works. Click To Tweet

The Migrating Motor Complex (MMC) can be stimulated with Prokinetics

Since deficiency of the MMC is the leading cause of SIBO, I thought it might be helpful to get some insight into how it works. Dr. Siebecker discussed MMC at length on the Healthy Gut Podcast with Rebecca Coomes, a podcast I highly recommend for anyone with SIBO. Here are some highlights from their discussion.

  • MMC happens in the small intestine.
  • It’s called the housekeeper wave.
  • It’s primary purpose is to clear the small intestine of bacteria via downward squeezing that pushes contents into the large intestine.
  • MMC only happens during fasting (2-4 hours after a meal). Dr. Pimentel and Dr. Siebecker advise leaving four hours between meals, without snacking, so MMC can activate. The doctors are not certain if coffee or water turn off MMC, but they are certain a meal does. For people who need to gain weight, Dr. Siebecker says fasting overnight, and maybe one other four-hour fast during the day, may be enough. Another approach is to eat really large meals, but then cut out snacking. Either way, being underweight takes precedence.
  • MMC is different than peristalsis, which is more of a mixing/churning motion to make sure food is presented to the walls of the small intestine. MMC facilitates food absorption. Peristalsis hardly pushes down at all. By contrast, MMC pushes down vigorously.
  • MMC stops about 2/3 of the way down the small intestine. The last third of the small intestine has it’s own motility with a different name. The large intestine also has it’s own motility. The motility that causes a bowel movement is called Mass Motor Movements (MMM). A person can still have diarrhea with impaired MMC if there is fast motility in the large intestine.
  • Some bile and enzyme secretion comes with MMC. These secretions are like soap and are meant to clean. Dr. Pimentel describes it as being like washing the dishes after a meal.
  • There is a 6-hour, expensive, invasive test for MMC called Antroduodenal Manometry. So far, it’s only available 3 or 4 places in the US. A less invasive test is being developed. It’s called the Acoustic Gastric Motility test.
  • Among people with nerve damage that results in impaired MMC, 50% spontaneously heal within 5 years. For the other 50%, it isn’t yet clear whether it remains due to new food poisoning, an autoimmune issue or other factors. The takeaway is that people do recover from the nerve damage.

MMC can be stimulated by a prokinetic drug or herbal compound. Prokinetics are usually given at bedtime because that’s the longest fast in a 24 hour period and provides the most opportunity for MMC to work. Prokinetics include:

  • Low-dose Erythromycin: 50 mg/day. Patients can develop a diminishing response and need to take a break from it.
  • Tegaserod (Zelnorm): 2-6 mg/day (taken off the market in the U.S.)
  • Prucalopride (Resolor/Resotran): 0.5-1 mg/day (taken off the market in the U.S.)
  • Low-dose Naltrexone (LDN): 50 – 300mg/day
  • Iberogast: A combination of nine herbs that can be used to treat both diarrhea and constipation, low to no side effects, and it is a proven prokinetic. Dr. Siebecker said she has good results in about 80% of IBS patients. She uses a dose of 20 drops 3 times/day. She did mention that some patients are sensitive to it and it can help to start with a lower dose and work up.
  • Ginger: 1,000 mg/day. Note that ginger is not appropriate for patients on blood thinners.

Thanks to Angie Alt at for her notes on prokinetics from the 2015 SIBO Symposium.

Laxatives are not prokinetics. Laxatives don’t stimulate MMC. But prokinetics can have a laxative effect.

This video shows how aggressively the MMC squeezes.

Stimulating MMC plays a vital role in resolving IBS from SIBO. Click To Tweet

Lab test for SIBO – Lactulose Breath Test (LBT)

Dr. Siebecker prefers a 3-hour lactulose breath test (LBT) for her patients. The advantage of a laculose test over a glucose test is that it can diagnose overgrowth in the distal end (latter 17 feet) of the small intestine, where overgrowth is thought to be more common. The test itself involves breathing into a small balloon, ingesting a precise amount of sugar, and repeating breath samples every 15 minutes for 3 or more hours.

Dr. Pimentel admits breath testing isn’t perfect, but it can tell you whether methane is high or not. He says, “…when you have methane on the breath test, that’s extremely predictive. Hydrogen is a little bit more challenging.”

Other functional medicine tests like the Organix Dysbiosis urine test or a comprehensive stool test can offer clues. They may lead your doctor to order a breath test. Another option would be to just begin treatment for SIBO since the treatment has little risk and costs less than the test.

If you have IBS, test for SIBO with a lactulose breath test. Click To Tweet

Kill SIBO with herbal antibiotics or Rifaxamin

While diet can be used to manage symptoms, antibiotics are needed to eradicate bacterial overgrowth. Most holistic practitioners will lean toward herbal antibiotics first, but pharmaceutical drug antibiotics also have their place.

Chris Kresser is a clinician that specializes in SIBO. His approach is representative of what I found among functional medicine practitioners. “We use both in our clinic.  We will tend to start with a botanical protocol, and if that’s not effective, we’ll go on to Rifaximin, or Rifaximin plus Neomycin if it’s methane.” (One of Dr. Pimentel’s studies showed that Combining Rifaxamin with Neomycin boosts efficacy from 45% to about 80%.)

It is not uncommon for more than one round of antibiotics to be required, so don’t be discouraged if you don’t achieve 100% eradication on the first try.

Here's how to kill the bacteria that give you IBS! Click To Tweet

Herbal antibiotics for treating SIBO

Several health centers, including John’s Hopkins, conducted a study that concluded, “Herbal therapies are at least as effective as rifaximin for resolution of SIBO” with “similar response rates and safety profiles”.

Dr. Siebecker says, “My associates and I have been using herbal antibiotics for SIBO since 2011.  We have consistently found them to be as effective as pharmaceutical antibiotics in relieving symptoms and reducing gas levels on breath testing.”

Herbs contain many different compounds, which can enhance their effectiveness. There’s also a synergistic effect when herbs are combined. This effect may help prevent resistance and target more microbes at once.

The effectiveness of herbs depends on what species of bacteria is overpopulated, where they are residing, your resistance and potency of the herb. Some trial and error is par for the course. Not all herbs that are effective against hydrogen producers are effective against methane producers. Many of the antibacterial herbs are also anti-fungal and anti-parasite. You can use this to your advantage since candida (in harmful fungal form instead of harmless yeast form) and parasites often accompany (or cause) bacteria overgrowth.

Here’s a list of herbal antibiotics from Herbal Encyclopedia.

Dr. Pimentel points out that herbal antibiotics are still antibiotics. Like pharmaceuticals, plant chemicals can also have side effects and negative consequences. Bacteria can still get resistant. Check cautions on Herbal Encyclopedia and, if necessary, consult with a practitioner that is qualified to advise on herb use.

IBS can be treated with herbal antibiotics like garlic, wormwood and clove. Click To Tweet

Herbal antibiotic protocols from doctors

Here are three herbal protocols used by our SIBO experts.

1. Protocol used by the multi-center team in the 2014 study

They used one of two herb combinations, so you would pick one.

  • Biotics FC Cidal – 2 capsules, twice per day (total of 4 capsules per day) for 4 weeks
  • Biotics Dysbiocide– 2 capsules, twice per day (total of 4 capsules per day) for 4 weeks

There’s also a more expensive combo:

2. Protocol published by Dr. Siebecker

1-3 of the following herbs for 4 weeks per course. Use the highest levels suggested on product labels.

3. A protocol from Dr. Michael Ruscio

Take throughout the protocol if tolerated.

  • Primal Defense from Garden of Life – This is a probiotic and prebiotic.
  • Digestzymes from Designs for Health – a blend of hydrochloric acid, pancreatic enzymes and bile. You can also do a straight hydrochloric acid supplement (cheaper) if you do better on hydrochloric acid. It is critical that one avoids anything that will inhibit stomach acid production like antacids, H2 inhibitors, and proton pump inhibitors.
  • Allimax Pro (optional) – An agent to help break down biofilms. More on biofilms later with two options that are far less expensive.

Month 1

Month 2

Three herbal antibiotic protocols for IBS, from doctors. Click To Tweet

Rifaximin (Xifaxan) and Neomycin

The most studied and successful prescription antibiotic for SIBO is rifaximin (brand name Xifaxan). A 2016 study found, “Rifaximin is a non-absorbable antibiotic with additional anti-inflammatory and gut microbiota-modulating activity.” According to Dr. Siebecker’s website, that means “…they stay in the intestines, having a local action and don’t cause systemic side effects, such as urinary tract infections. They are chosen specifically for this property which allows them to act only where they are needed.”

Rifaxamin considerations:

  • Rifaximin may be used for all cases of SIBO.
  • Neomycin is effective for constipation cases and is used in addition to Rifaximin. Metronidazole is an effective alternative to Neomycin, currently under study at Cedars-Sinai.
  • If alternating diarrhea is present with constipation, the use of Rifaximin alone has been suggested.
  • A course of pharmaceutical antibiotics typically lasts two weeks while a round of herbal antibiotics takes four weeks.
  • Sometimes Rifaxamin and Neomycin are covered by insurance. Botanicals usually are not.
  • Rifaxamin and Neomycin are only available by prescription.
  • SIBO often recurs and can require treatment several times in a year. Most holistic medicine practitioners would prefer not to prescribe pharmaceutical antibiotics that often.
  • “…short-term repeat treatment with rifaximin is not associated with the emergence of significant bacterial resistance.” (study)

You can print out full dosing options for your doctor here on

IBS from SIBO can be treated with Rifaximin and Neomycin. Click To Tweet

May be helpful in all protocols

From the Textbook of Functional Medicine (page 215): “Regular exercise also helps in maintaining proper peristaltic action and promoting proper transit time.”

Atrantil can help starve archaea

If you are suffering from methane-induced bloating and/or constipation, there’s a botanical product that a 2016 study found 88% effective in reducing symptoms. It’s called Atrantil.

Atrantil contains flavonoids from quebracho extract (a South American hardwood tree). The flavonoids soak up hydrogen and starve archaea of it’s food source. Without their hydrogen food source, archaea are unable to convert hydrogen into methane. When methane is reduced, it has less ability to slow motility. Also, without their food, archaea die off or leave.

Atrantil was found 88% effective in reducing IBS symptoms. Click To Tweet

Do a two-week elemental diet instead of, or right after, antibiotics

You don’t want to try an elemental diet during antibiotic treatment because the bacteria will go into hibernation. This option would be used immediately after an antibiotic protocol.

The Elemental Diet removes all solid food for two to three weeks and consists of nothing but powdered nutrients mixed with water. This starves out the bacteria as nutrients in this form are absorbed so quickly that the bacteria don’t have a chance to consume them.

Physicians’ Elemental Diet is a blend I found that is free of typical allergens like gluten, corn and soy.

Here’s a video from Dr. Siebecker explaining how to do the elemental diet.

Dying bugs release toxins

The official name for this is Herxheimer Reaction. Another common description is die-off effect.

According to Functional Medicine University, “The toxic by-products of the microbes can circulate and recirculate through the blood and lymphatics, causing possible symptoms of die-off such as fatigue, achiness, fever, and difficulty with concentration, sometimes resembling a mild case of the flu.”

Die-off means the protocol is working. My personal experience with die-off was two days of heavy brain fog. Then it cleared up and SIBO symptoms improved significantly.

A binding agent like activated charcoal can help reduce the severity of the die-off effect. I use Bulletproof Activated Coconut Charcoal.

Diet during SIBO treatment

The primary foods of gut bacteria overgrowth are sugar, starches, fermentable carbohydrates, prebiotics and soluble fiber. The scienc-y description is Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols. Most people have trouble remembering those big words, so instead use the acronym: FODMAP.

Now it’s true that if you have a lot of FODMAPs in your diet, bacteria will multiply quickly and symptoms will increase. Starving the critters does make it harder for them to produce gas and toxins. Thus, temporarily reducing or eliminating FODMAPs often reduces symptoms quickly.

Does that mean we want to eliminate FODMAPs during SIBO treatment? There’s debate on this. Dr. Pimentel says, “…happy and well-fed bacteria, are more sensitive to antibiotics and are easier to kill. What that means is that most antibiotics work on the replicating cell wall of bacteria. When bacteria are in hibernation, starving, distressed, they wall off, don’t replicate, and they just sit there, waiting for conditions to improve.  That’s a survival mode. So when the bacteria are in survival mode, antibiotics won’t penetrate and won’t work as well.”

Dr. Siebecker and others have found many of their patients can’t handle the symptoms produced by well fed bacteria. They will advise removing foods that make the patient uncomfortable. Here’s wording that, I think, fairly represents both perspectives.

While taking herbal or pharmaceutical antibiotics to eradicate SIBO, eat as many FODMAPs as you can tolerate and still function.

Preventing SIBO recurrence

A set of conditions led to SIBO in the first place. Prevention involves not resetting that stage. Here are some prevention suggestions.

  • Follow the diet and lifestyle recommendations in the Wellness Repair Plan.
  • Stimulate MMC with a prokinetic and physical activity.
  • Reduce FODMAPs or any food that causes symptoms to flare.
  • Supplement with Hydrochloric Acid (HCl), the antibacterial acid of the stomach, if deficient.
  • Treat diseases that contribute to SIBO.
  • Manage stress, including the stress caused by food intolerances that activate your immune system.

What if SIBO recurs within a couple weeks? Dr. Pimentel says, “When the patients relapse in one week or two weeks, then we start to be concerned that it isn’t just a motility disorder, that maybe it’s an adhesion or some other mechanical cause for the overgrowth to begin with and not just the motility disorder.”


  • IBS predisposes SIBO. If you have IBS, SIBO is highly likely.
  • Bacteria produce gas. Gas correlates to symptoms.
  • The main cause of SIBO is deficiency of the Migrating Motor Complex (MMC), a downward squeezing action of your small intestine.
  • You can stimulate MMC with a prokinetic drug or with herbs like Iberogast or ginger
  • The lab test for SIBO is a 3-hour lactulose breath test (LBT)
  • Kill SIBO in four weeks with  herbal antibiotics or in two weeks with Rifaxamin. See above for exact protocols recommended by doctors.
  • Atrantil was 88% effective in reducing symptoms of those suffering from methane-induced bloating and/or constipation.
  • If you do an elemental diet, do it after antibiotic treatment instead of during. Antibiotics work best when the bugs are eating instead of hibernating from starvation.
  • Prevent recurrence of SIBO with lifestyle adjustments like following the Wellness Repair Plan.

Additional Resources

Steven Sandberg-Lewis, ND, DHANP

Dr. Steven Sandberg-Lewis has been a physician for over 40 years. He practices at the National College of Natural Medicine (NCNM) Teaching Clinic where he specializes in gastro-intestinal conditions, including inflammatory bowel disease (IBD – including microscopic colitis), irritable bowel syndrome (IBS), Small Intestine Bacterial Overgrowth (SIBO), gastroesophageal and bile reflux (GERD), biliary dyskinesia, and chronic nausea.

He is the author of the medical textbook: Functional Gastroenterology: Assessing and Addressing the Causes of Functional Gastrointestinal Disorders

Dr. Sandberg-Lewis also co-authored an article for the Townsend Newsletter with Dr. Siebecker called SIBO: Dysbiosis Has A New Name.

Podcasts about SIBO

The Healthy Gut – Hosted by Rebecca Coomes

The SIBO Doctor – Hosted by Dr. Nirala Jacobi, BHSC, ND


0 replies

Leave a Reply

Want to join the discussion?
Feel free to contribute!

What didn't I cover that would help you? Please leave a comment to let me know and I'll try to fill in the gap for you.