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Digestive complaints are among the most common issue I hear, true of almost every client with whom I work. One of the more common complaints is, by the end of the day, I look six months pregnant!

Bloating can of course be caused by many factors– candida, parasites, pathogenic bacteria, food intolerances– but if you find your bloating worsens over the course of the day, you experience painful bloating after every meal, or if you are bloated after meals where you think you’re even avoiding the hard-to-digest foods like gluten and dairy, your problem could be small intestine bacterial overgrowth or SIBO.

What is SIBO?

We have trillions of bacteria–both good and bad–predominantly in our large intestine. But when there are too many bacteria in the small intestine particularly, it’s a different ballgame. The small intestine is fairly sterile and shouldn’t really be home to much of the bacteria present in the large intestine, so when bacteria migrate up and take root there, symptoms such as pain, bloating, belching, abdominal distention, reflux, constipation and/or diarrhea result as the bacteria ferment the carbohydrate fibers you eat. SIBO symptoms present similarly to candida or leaky gut, but there are a few differences.

Here are the Main Signs of SIBO

  • Gas & Bloating, especially after a meal with fiber, sugar, starch
  • Carbohydrate intolerance, feeling like you can’t tolerate vegetables or starches
  • Abdominal pain, bloating, or cramping after a meal, and you’re not sure what’s causing it
  • Feel worse after taking probiotic, which exacerbates symptoms
  • Constipation
  • Taking fiber worsens symptoms
  • Chronic Diarrhea
  • B12 deficiency or low iron
  • Multiple food intolerances
  • Heartburn/reflux
  • Belching
  • Bad bout of food poisoning, and you haven’t felt quite right ever since
  • Eczema and skin rashes
  • Rosacea

Some of the key differences in symptoms that tell you it’s SIBO specifically are

  • excessive belching
  • bloating which worsens over the course of the day, looking pregnant by day’s end
  • bloating or pain with probiotics (which feed the bacteria in the small intestine, causing pain to worsen)
  • frustration because you’re not sure what’s causing your bloating or gas
  • not feeling relief after going gluten and dairy free
  • chronic constipation or alternating constipation/diarrhea

I have many frustrated new clients that come in feeling discouraged because they’ve cut out gluten and dairy and/or they’re eating mostly paleo but still having symptoms. That’s a major bummer and typically represents a microbiome imbalance.

SIBO is present in a high percent of Crohn’s, Celiac, and IBS cases and could be a cause or contributing factor to these conditions. These folks do very well on a low FODMAP diet.

So What Causes SIBO?

The most common causes are

  • slow gut motility in the small intestine: Our migrating motor complex (MMC) should clear bacteria from the small intestine, sweeping it down toward the colon, both overnight and when we’re fasting, but if the MMC is compromised in any way, bacteria migrate up and remain in the small intestine. These misplaced bacteria take root in the small intestine, and they and love carbs and starches as their main food source. They eat and ferment your food (contributing to deficiencies) and multiply, contributing to the pain and bloating from gas that gets trapped in the small intestine as the bacteria are fermenting the carbohydrates/fibers you ate.
  • structural issue: adhesions, partial obstruction in the small intestine that causes bacteria to back up; illeocecal valve issues
  • colon surgery: Patients with colectomy demonstrate significantly higher prevalence of SIBO (source)
  • immunodeficiency disease (weakened immune system)
  • food poisoning (gastroenteritis): causes dysfunction in the MMC because nerve cells can be destroyed by food poisoning
  • antibiotic use
  • steroid drugs
  • acid-blocking drugs (PPIs) which decrease your hydrochloric acid production
  • hypothyroidism, which slows the MMC

Slow gut motility is a main factor. There are many causes of slowed gut motility, including food poisoning, drugs like PPIs, hypothyroidism, certain diseases, adhesions, antibiotics, and inflammation that destroys motility.

A very common pattern I see is SIBO taking hold after a bad bout of food poisoning. Interestingly, up to 80 percent of SIBO cases are caused by food poisoning. These folks will come in and say they haven’t felt the same since the food poisoning incident, yet all stool tests come back clean (SIBO isn’t detected via stool test). This is because the MMC is malfunctioning, allowing bacteria to creep up to the small intestine.

SIBO is also common with hypothyroidism (estimated at up to 54%) because a sluggish thyroid = slowed gut motility that can allow those bacteria to migrate into the small intestine.

Who Gets SIBO?

  • 66% of Celiac patients (who exhibit above symptoms)
  • 15% of the elderly population
  • 90% of alcoholics
  • 53% who use antacids chronically
  • 80% of IBS patients
  • 33% with chronic diarrhea
  • hypothyroid patients (don’t have stats on this)
  • history of chronic antibiotic use (no stats on this)


How to Test for SIBO

You can test for SIBO, but you will need a dedicated breath test. SIBO will not show up on the conventional stool test we use to detect pathogens and parasites, because that test assesses the large intestine. You need to test the small intestine via breath testing.

On a stool test, you may notice high levels of certain strains of bacteria in the gut, and that may point to SIBO, but the only way to confirm SIBO is via lactulose breath test: you’ll need to drink a prepared lactulose solution, then methane and hydrogen gases are measured within 2-3 hours. The bacteria in the small intestine ferment the sugar in the lactulose solution and release methane, hydrogen or hydrogen sulfide gases in response. When these gas levels are higher than they should be, you are positive for SIBO.

You can order your own breath test here, but you’ll need a qualified practitioner to interpret the results for you. You can also order (through a doctor) the brand new trio smart breath test which tests for all 3 types of SIBO.

Types of SIBO

Your breath test will indicate if you have

  • hydrogen dominant SIBO (often causes diarrhea)
  • methanogen overgrowth, which can also occur in the large intestine, unlike the other types of SIBO
  • both hydrogen & methane
  • hydrogen sulfide, which often causes diarrhea and sulfur intolerance

Methanogen overgrowth (previously known as methane dominant SIBO) is typically associated with constipation, while hydrogen dominant SIBO correlates with diarrhea or no symptoms at all. Hydrogen sulfide SIBO, which is typically indicated by a complete flat line pattern on a regular breath test, correlates with excess hydrogen sulfide gas, diarrhea, and sulfur intolerance.

NOTE that methane dominant SIBO is now known as intestinal methanogen overgrowth (IMO), which is really more accurate, as the methanogens that produce methane gas are not bacteria. IMO is the most common type I see. Read my post on it here.


Note on treatment: SIBO is one of the hardest gut issues to eradicate. I highly recommend working with a skilled practitioner on this, because it requires a very specific protocol and follow-up treatment. SIBO very easily recurs if there is not proper followup.

Although SIBO has no doubt been affecting humans throughout history, the research on it is fairly new and ever evolving (hence the name change from methane dominant SIBO to intestinal methanogen overgrowth since methane gas producing microbes are actually archaea and not bacteria). I also suspect SIBO is also becoming much more prevalent due to an increase in hypothyroidism, overall inflammation, antibiotic and antacid use, and poor diets.

As with candida infections, the best way to treat SIBO is to starve it and kill it. You can use antibiotics like rifaximin and/or neomycin (from your doctor) or anti-microbial herbs. I’m beginning to see that the herbal protocols are more effective in the long run, but these protocols take longer. For tough cases, antibiotics followed by herbal protocols work best.

If you get antibiotics from your doctor, PLEASE be aware that you must follow-up the antibiotics with treatment to address poor gut motility, or the SIBO will recur. I see these cases all the time. People get quick relief with antibiotics, but there can be a very strong (I’ve heard up to 100 percent) recurrence rate after 3 weeks if you leave it at that. I believe this is true because there is no follow-up prokinetic treatment to fix the MMC, which is crucial to prevent recurrence. If your doctor does not mention any after care or prokinetic treatment, find a new doctor.

Diet: Many people find relief eating a low FODMAP diet. Click here to read all about FODMAP foods and how to avoid them. SIBO diets are tricky because everyone’s healing diet will look different, as will the timing of particular foods to include and avoid. Here is my article on how to determine your ideal SIBO diet.

Most importantly, make sure you’re avoiding sugar, alcohol, refined foods, and gluten. Avoid coffee, which is a gut irritant, if you can do it. The eventual goal is to remove the starches that feed the bacteria. The exception is during the anti-microbial herb or antibiotic protocols when you actually want to encourage the bacteria to be more active (source). I recommend a paleo-type plan during the protocols, as they’re the best to reduce inflammation in the GI tract, then some variation of a low fermentable starch plan for three months following treatment. For severe cases I may recommend an elemental diet. I don’t recommend a low FODMAP plan longterm because it depletes needed short chain fatty acids in the gut.

Herbs: I use various herbal combos with berberines, like this one, and other bacteria-killing herbs. Garlic and oregano oil work great, too, but the ideal protocol depends on if you’re methane or hydrogen dominant and which herbs you can tolerate. I use this one and this one if the person has SIBO and yeast overgrowth. This supplement is excellent to add to a protocol for methane dominant SIBO if the person is experiencing bloating, and I often recommend it during the 3 month follow-up to the herbs to prevent recurrence. I sometimes use neem as well.

Opportunistic bacteria that take over when the gut flora becomes unbalanced create strong mesh-like structures called biofilms where they reside, hide from the immune system, thrive and multiply (source). For this reason, I may recommend a biofilm disrupting supplement, especially if yeast overgrowth is an issue. I use Biocidin or N-acetyl cysteine, BUT some SIBO experts think the biofilm agent isn’t needed. I evaluate on a case by case basis. You must also use a prokinetic agent after treatment to make sure your gut motility prevents bacteria from migrating back up to the small intestine. This is probably the most important point of treatment.

A round of herbs is about 4 weeks long, and often several rounds are needed depending on your test results and the level of overgrowth.

Be aware that you may need up to 3 rounds of herbs to completely wipe out SIBO, depending on how high your gas levels are, as indicated by your breath test. A single round of herbs or antibiotics reduces gas levels by about 30ppm. 2 weeks of the elemental diet may reduce SIBO gases by up to 150ppm, so I usually recommend that for severe cases.

Follow-up: It’s really important to use the prokinetic agent for up to 3 months post treatment to prevent recurrence. AND figure out the underlying cause in the first place to prevent regrowth. I use both Iberogast and Motility Activator for prokinetics, depending on if the person suffers with constipation or diarrhea. I’ll also recommend a soil based probiotic and leaky gut healing support, such as glutamine and zinc carnosine.

Other Resources

Dr Siebecker’s excellent info on SIBO
Pimentel/Kresser interview
Siebecker interview on SIBO + causes
Everything you need to know about SIBO
10 signs you have SIBO
Excellent SIBO series all about causes and treatments

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