What is SIBO? The Symptoms, Testing, and Natural Treatments.

Get relief from bacterial overgrowth with effective herbs, nutrients, and diet.

Your large intestine (colon or large bowel) is about 5 feet long and about 3 inches in diameter. It is the home of billions of bacteria that help complete digestion. This phase of digestion lasts for about 33 hours before you have a bowel movement.

Too many undigested carbohydrates can cause an overgrowth of bacteria into the small intestine (where bacteria do not belong). This can cause nutrient malabsorption and digestive symptoms. When this happens, you may start to experience wide-ranging disease patterns such as IBS/IBD, chronic fatigue syndrome, Celiac Disease and fibromyalgia. More than 50 associated diseases overlap with SIBO!

  • Do you have episodic joint pain and your muscles hurt all day long?
  • Do you feel better on antibiotics and/or suspect that you have a stealth pathogen like Lyme’s disease?
  • Do you remember the last time you had a “normal” bowel movement and are convinced that certain kinds of foods like gluten and dairy have ruined digestive system?
  • Do you have chronic constipation and feel that it takes you longer than others to have a bowel movement?
  • Did removing carbohydrates make you feel better for a spell, but then to reach that same great feeling, you need an even more restrictive diet?
  • Do you have lots of unresolved gas?

Do you have SIBO and have been wrongly diagnosed?

Because of the wide-ranging symptom patterns, SIBO is being wrongly diagnosed as chronic fatigue syndrome, food intolerances, estrogen dominance, fibromyalgia, IBS, and Lyme’s Disease. Many times, symptoms are seen after antibiotics or abdominal surgery.

Reported Prevalence of Small Intestinal Bacterial Overgrowth

  • Fibromyalgia 93%
  • Crohn’s disease up to 88%
  • Ulcerative Colitis 81%
  • Chronic Fatigue Syndrome 81%
  • Irritable Bowel Syndrome up to 78%
  • Gastrectomy 63-78%
  • Hypochlorhydria (drug-induced) up to 78%
  • Celiac disease up to 67%
  • Connect Tissue Disease (e.g. Scleroderma) 43-55%
  • Hypothyroidism 54%
  • Rosacea 46%
  • Diabetes Type II up to 44%
  • Obesity up to 41%

Why do Bacteria Overgrow into the Small Intestine?

There are two simple reasons why bacteria typically bloom (overgrow):

  1. Poorly Digested Food. Too much undigested food that is not digested by acids and enzymes will become “bug food”. The SIBO variety will especially love the undigested carbs.
  2. Antibiotics. Your microbiome should have diverse colonies of bacteria that balance each other out. Antibiotics can destroy both good and bad bacteria, causing certain bacterial strains to be able to overgrow and “crowd out” other strains. This is seen by low diversity of bacteria as seen by a common stool test. It has been shown that antibiotics alone can cause SIBO, especially with Clostridium dificille infection (CDI).

According to Bradley Bush, ND Medical Director of Neurovanna, “SIBO is not a single, but a grouping of various large intestinal bacteria species including E. coli and Klebsiella. These gut bacteria are not normally exposed to carbohydrates and sugars which are plentiful in the small intestines. Sugars and carbohydrates act like a fertilizer and make SIBO very active.”

“Gut bacteria are not normally exposed to carbohydrates and sugars which are plentiful in the small intestines. Sugars and carbohydrates act like a fertilizer and make SIBO very active.”

He goes on to say, “Not only do they continue growing, they also displace your normal small intestinal flora. SIBO also releases a number of chemicals and gasses that are not normally found in the small intestines and include hydrogen gas, methane gas and ammonia. Unlike the large intestine, the small intestines normally have a small number of bacteria and if they become overgrown, these organisms will use up the nutrients that would otherwise be absorbed into the body.”

Aerophilic Strains

  • Streptococcus
  • Escherichia coli
  • Staphylococcus
  • Klebsiella

Anaerobic Strains

  • Bacteroides
  • Lactobacillus
  • Clostridium

Measuring Methane and Hydrogen

Hydrogen and Methane are not made by humans but by bacteria in the large intestine after consuming carbohydrates such as lactulose and glucose.

Practitioners measure the amount of these gases (that’s made by bacteria, not humans) to understand how progressed up the intestine the SIBO has become.

Farmers are starting to feed cows oregano to reduce SIBO and methane.

Most of the current research into methane and hydrogen has been done on dairy cows. They are ideal animals to study because cows eat literal tons of carbohydrates a year, and if the cow has bacterial overgrowth, produce tons of methane. Not only is methane a greenhouse gas, but signals problems with the cow’s gastrointestinal system.

Dairy farmers do not like excess methane because to get the same milk production, they have to feed the animal more. It is referred in research as “energy loss”.

Recent experiments (2015) demonstrated that inhibitors (such as garlic oil) persistently decreased enteric methane emissions without negatively affecting animal productivity. This extra energy was used for building tissue and led to greater body weight.

What you will quickly realize is that herbs, nutrients, enzymes that work at reducing methane gas, may not work on bacteria that produce hydrogen gas. This is why it can be valuable to do the breath test. Let’s learn a little bit more about testing options that can lead to more effective and inexpensive protocols.

What Testing Options Are Available?

Symptoms for SIBO overlap with many different disorders from Lyme’s Disease to Adrenal Fatigue, therefore, testing can be quite valuable to understand what the heck is going on. The goal of testing should be to rule out SIBO. If it is SIBO, then you should find out if you have elevated hydrogen, elevated methane, or both. This will help you understand which herbs will be helpful.

Glucose Breath Test (GBT)

Following a special diet that removes food that would feed bacteria and a 12-hour fast, you drink a glucose (sugar) and water mixture. 6 measurements are taken, one before the drink, then five after in 20-minute increments.

If bacteria digest the glucose within the first 3 feet of your small intestine, then methane (M) and hydrogen (H) gas circulate into your bloodstream through your small intestine and is expelled through your lungs. This test is used to diagnose overgrowth in the first two feet (proximal) of your small intestine.

Lactulose Breath Test (LBT)

Following a special diet that removes food that would feed bacteria and a 12-hour fast, you drink a lactulose (sugar) and water mixture. 6 measurements are taken, one before the drink, then five after in 20-minute increments.

You cannot digest lactulose, only bacteria have the enzymes to do this. After the bacteria digest the lactulose, they create hydrogen and methane gas. The gas diffuses into your bloodstream from your small intestine and is expelled through your lungs. The test measures the amount of H and/or M. This test is used to diagnose overgrowth in the end (distal) of your small intestine.

What does Lyme’s Disease have to do with SIBO?

Lyme’s disease has many of the same symptoms as SIBO. This can be a chicken and egg problem because antibiotics share the exact same symptoms as SIBO and all patients get heavy antibiotic loads after Lyme’s Disease diagnosis. Symptoms are very important determinant in this disease since 56% of patients with Lyme disease test negative using the testing system recommended by the CDC.

Lyme’s Disease is typically spread by infected ticks with a Babesia or Bartonella infection… and now Borrelia.

In early 2016, Mayo Clinic researchers shared their research about a new bacterial species called Borrelia mayonii that caused Lyme Disease. It was detected in the Upper Midwest.

Bacterial strains that are seen with Lyme’s Disease, Borrelia mayonii and Borrelia burgdorferi. They each present a different rash and both have GI side effects like vomiting and nausea. Borrelia burgdorferi presents with a diffuse rash. Borrelia mayonii presents with a bulls-eye rash.

While existing lab testing can detect B. mayonii, only a genetic-based PCR test will be able to tell the difference between the two. Conventional treatment of high dose antibiotics and herbal antibiotic treatment is used for both species.

Use Caution When Using Antibiotic Treatments!

  • Increased risk of Clostridium dificille infection (CDI) when using antibiotic treatments. IBD patients are at an increased risk.
  • May result in a rebound effect on gut bacteria. Post antibiotic treatment resulted in a dramatic increase in concentrations of mucosal bacteria.
  • IBD in children is associated with antibiotic usage.
  • Antibiotic resistance is becoming more common and bad for the health of your community.
  • Antibiotics for SIBO are very expensive and are not as effective as herbal approaches.

What is the Natural Herbal Treatment for SIBO?

Functional Digestion Specialists are using cycling “Weed and Feed” protocols with herbs and nutrients that:

  • Have Antibiotic Properties
  • Target “Stealth Pathogens”
  • Improve Short-Term Motility (constipation)
  • Reduce Methane and Hydrogen Gases
  • Improve B12 and Fat-Soluble Vitamins (A, D, E and K)
  • Support the Mucous Membrane
  • Inoculate Beneficial Bacteria

Protocols are typically administered for a minimum of 90-days to reduce the bacterial overgrowth, create a healthy pH of the small and large intestines, reduce inflammation and repopulate healthy bacterial strains. It is recommended that you retest after the 90-days before doing another cycle to see if you are headed in the right track.

“People with SIBO may become malnourished as a result and often feel better after a short round of Myers nutritional IVs.”

Top Herbs for SIBO

Thanks to advances in bacterial testing and herbal research, there are many options available for naturally treating SIBO. Many practitioners utilize a Weed and Feed approach because it reduces the risk of severe bacterial die-off and subsequent symptoms.

Herbal therapies are very effective. A recent landmark study concluded that, “Herbal therapies are at least as effective as rifaximin for resolution of SIBO by LBT. Herbals also appear to be as effective as triple antibiotic therapy for SIBO rescue therapy for rifaximin non-responders.” Here are our picks for the more researched herbs available from our practitioner network:

Oregano (Origanum vulgare) Leaf Essential Oil Extract

Oregano is an herb that we take for granted because it is used to season our pizza and pasta, but few know the amazing antibacterial properties and is well-known to treat athlete’s foot and bacterial overgrowth. It is very strong when delivered as an essential oil and needs to be enterically coated (intact until delivered into the intestine) for the purposes of treating SIBO.

According to WebMD, “Taking oil of oregano for 6 weeks can kill the parasites Blastocystis hominis, Entamoeba hartmanni, and Endolimax nana.”Researchers at Aarhus University in Denmark recently (2016) studied the power of Oregano to reduce methane in Dairy Cattle, “Oregano has essential oils with a mild antimicrobial called carvacrol, which can kill some of the bacteria in the cow’s rumen that produce methane.”

Warning: Oregano leaf extracts can cause reactions in people allergic to Lamiaceae family herbs, including basil, hyssop, lavender, marjoram, mint, and sage (moderate level of risk).

Caution: It also might lower blood sugar levels; therefore, diabetics should monitor their blood sugar while taking this useful herb. It might also increase the risk of bleeding when taken in high doses, so stop 2-weeks before surgery. Monitor (low level of risk).

Anise (Pimpinella anisum) Fruit Essential Oil

Anise fruit is a carminative, an herb intended to prevent formation of gas in the gastrointestinal tract. According to a 2012 review of this herb, Anise has effective antibacterial, antifungal, insecticidal, and antiviral properties. It has properties that also help relax smooth muscle, so it is a great mild laxative. A study also shown Anise to be as effective as 100mg of aspirin for pain relief, which can be extremely helpful in painful IBS cases.

Warning: Do not use in pregnancy and lactation at very high doses of the essential oil (870-1400 mg/kg). Avoid in those with sensitivity to anethole.

Caution: At an oral dose of .5 mL or above use caution in alcoholism, estrogen-dependent cancers, liver disease, pregnancy, lactation, and endometriosis.

Interaction with Drugs: At an oral daily dose of .5 mL or above, use caution in those taking acetaminophen.

Andrographis (Andrographis paniculate) Leaf Extract

Andrographis has “biological activities including anti-microbial, anti-inflammatory, anti-oxidant, anti-diabetic, cytotoxicity, immune modulatory, sex hormone modulatory, liver enzyme modulatory, anti-malaria, anti-angiogenic and hepato-renal protective activity.”Andrographis extracts are currently used to treat inflammatory diseases like Ulcerative Colitis (UC) and IBD that are often associated with SIBO.

A 2013 double blind, placebo-controlled trial demonstrated its safety and effectiveness for remission and mucosal healing in patients with mild to moderate UC. The study showed andrographis was as effective as Mesalamine. Andrographis is dose dependent, so more is better; 1,800 mg daily was more effective than 1,500 mg daily. In this study, 34% of study participants were in remission after week 8. Andrographis has also been shown to accelerate carbohydrate absorption by increasing brush-border membrane-bound enzymes lactase, maltase and sucrase in the small intestine of rats.

Warning: Do not use in pregnancy and lactation.

Caution: Andrographis is non-toxic, but can cause vomiting, gastric discomfort, and loss of appetite is high doses.

Phellodendron (Phellodendron amurense) Stem Bark

Phellodendron contains high amounts of berberine. In a study published in The Journal of Microbiology and Biotechnology, Berberine from Phellodendron amurense bark showed an ability to stop the growth of “bad” bacteria (Clostridium perfringens, Escherichia coli, and Streptococcus mutans) without effecting the growth of “good” bacteria (Bifidobacterium bifidum, B. longum, and Lactobacillus acidophilus).

According to The Journal of Infectious Diseases,  “Tests of the antiseptic action of berberine against bacteria, yeasts, viruses, and amoebas have shown a range of activity levels from apparent potent action to mild suppression.”

Garlic Bulb Extract Containing Alliin (enterically coated)

Powerful antibiotics can lead to resistance and do not differentiate between “good” and “bad” bacteria such as vancomycin-resistant enterococci (VRE) and methicillin-resistant Staphylococcus aureus (MRSA). A study conducted by Jaya Prakash and colleagues at the National University of Health Sciences in Lombard, IL, found that allicin has potent activity against VRE in vitro. In vitro testing showed that microgram quantities were sufficient to significantly inhibit the growth of VRE. SIBO sufferers tend to have painful IBS and need inflammatory support.

Garlic is also proven to be a key Nrf2 Activating Herb (anti-inflammatory).We recommend finding an enterically coated version to make it into the intestines since stomach acid breaks down the active ingredient allicin.

Warning: Contraindicated in known allergy to Garlic. Contraindicated in lactation. Discontinue 10 days before surgery.

Caution: Can cause diarrhea, vomiting, heartburn, nausea if taken on an empty stomach.

Golden Seal Root & Rhizome (Hydrastis canadensis) Extract

Golden seal is used to support healthy mucus function and membrane health. It is also a potent antiviral and antibacterial agent. This product has a very strong flavor and may be preferred as a tablet. Can be used in a liquid blend with Marshmallow root and Chamomile. Should contain at least 40 mg of hydrastine and 40 mg of berberine. Most liquid extract contain ethanol alcohol.

Warning: Adulterated herbs do not contain hydrastine that is unique to Golden Seal and provides the mucus membrane support.

Caution: Potential drug interaction with drugs that displace the protein binding of bilirubin (e.g. phenylbutazone). May potentiate effect of drug. Monitor (low level of risk).

Contraindicated: in pregnancy, lactation and patients with high blood pressure (moderate level of risk).

Diet Recommendations

Individuals who have SIBO often easily correlate what they are eating with the symptoms they are experiencing. Many find eliminating gluten (from grains) and lactose (from dairy) and using different diets such as Paleo, Atkins, GAPS, and bone-broth diets to be very helpful.

The Digestive Rebuilding Smoothies

Depending on how well you are digesting protein, fat, or carbohydrates, you have a choice of smoothies based on your digestive type. We have two recipes for fat types, two for carbohydrates, and two for protein.

Digestive Rebuilding Smoothie Recipes have extremely high nutrient density per calorie, meaning that they really pack a punch. We selected the ingredients in the smoothies for their phytochemical and enzymatic content. Simple and affordable, the smoothies are an excellent way to start your day and rebuild your digestion.

General Dietary Considerations

A combination of the Digestive Rebuilding Smoothie and Elimination Diet may be used during the 90-day program.

  1. REDUCE sugar, refined and fermentable carbohydrates (see SCD Diet), and red meat.
  2. REMOVE mucosal irritants such as alcohol, coffee, GMO foods, cow’s dairy, gluten, unsprouted grains, NSAIDS and trans fats.
  3. INCREASE bone broth, raw cultured dairy, fermented vegetables, cooked/steamed/roasted vegetables, coconut products and sprouted seeds. For non-responsive cases, Specific Carbohydrate Diet (SCD) and the low FODMAP diet can be recommended for the short-term.

Nutritional Deficiencies from SIBO

  • Fat-soluble vitamins (A, D, E, and K) deficiencies because small bowel bacteria can deconjugate bile salts.
  • Vitamin B12 (Cobalamin) due to an increased synthesis of folate by small intestine bacteria.
  • Trace Minerals deficiencies because of high bacterial fermentation.

Is Your Natural SIBO Protocol Working?

Many individuals notice positive health changes right away. They report using less toilet paper, gaining mental clarity, having better formed stools, reduction of gas and bloating, and a marked reduction of muscle pain.

SIBO protocols have been proven to be very effective. Unfortunately, because of their effectiveness, symptoms can worsen in the beginning of the treatment. This is because of a of bacterial die-off.

One of such die-off is called the Jarisch-Herxheimer (‘herx’) reaction. According to researcher Michelle Morgan, “Symptoms of the reaction can include headache, fever, chills, sweating, malaise, and hypotension (low blood pressure). This reaction has been associated with antimicrobial treatment of infections such as syphilis and Lyme disease. Thought to be the result of endotoxin release from the dead or dying bacteria and an increase of inflammatory cytokines.”

If you need additional support beyond this article and do not have a practitioner who is helping you navigate SIBO and get you the right herbs listed in this article, then we welcome you to find someone who can. Find a Functional Digestion Specialist here.


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Get Your Functional Digestive Assessment

Our 5-minute ‘yes’ or ‘no’ questionnaire will give you a 6-page educational report. Start your journey to feeling great, looking better, and living longer by addressing your digestive health.

Get Your Functional Digestive Assessment

Our 5-minute ‘yes’ or ‘no’ questionnaire will give you a 6-page educational report. Start your journey to feeling great, looking better, and living longer by addressing your digestive health.