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SIBO and IBS Demystified

Adapted from The Microbiome Connection by Dr. Mark Pimentel and Dr. Ali Rezaie. Published by GoodLfe, 2022.

An estimated 70 million people in the United States are affected by SIBO, IBS, or one of the more than a dozen other diseases linked to digestive health, and 74% of Americans say they live with symptoms of digestive discomfort (Pimentel 04). To me, this is unacceptable because I know that digestive dysfunction can (more often than not) be addressed and resolved without the use of powerful antibiotics, acid-reducing medications, and Metamucil, and instead with changes in diet, lifestyle, testing, and in severe cases, nutritional supplements. I have been working with an increasing number of patients who are experiencing digestive discomfort, and have been continuing my education and deepening my understanding of the gut. I recently read The Microbiome Connection by Dr. Mark Pimentel, MD, FRCP(C) who is professor of medicine and gastroenterology at Geffen School of Medicine UCLA and associate professor of medicine at Cedars-Sinai, Los Angeles, and Dr. Ali Rezaie, MD, MSc, FRCP(C), the medical director of the GI Motility Program at Cedars-Sinai, Los Angeles. Both of these doctors are very well respected and have been conducting ground-breaking research together in this field for decades. The book is very readable, and provides explanations of what happens to IBS/SIBO patients from the first diagnosis to the end of treatment. They also explain what changes can occur in the body in terms of the underlying physical processes to symptoms that may develop; and share evidence-based management and treatment of those symptoms through dietary changes and drug treatment. These are basically my notes from the book and the key points in understanding the differences between SIBO and IBS.

Setting the stage: your body has microbiomes on your skin, mouth, vagina, and your gut is actually home to your body’s largest microbiome - trillions of bacteria, viruses, and fungi that collectively weigh two pounds.  One gram of stool contains 100 billion microbes and half of them are alive.  (Pimentel 45).   Everything you eat affects your microbiome. In fact, the largest collection of lymphoid tissue in your body is actually located in your small intestine where the gut reacts to what you eat.  This is known as the “GALT” - (gut associated lymphoid tissue). Having your immune system in your gut is actually quite good because it protects you against the myriad of invaders that enter your body through your mouth.  The main causes of IBS are actually food poisoning or parasitic infections.   Our immune system may struggle to recover fully, and may end up with IBS, SIBO or both. One in nine people who experience food poisoning go on to develop IBS because  harmful pathogens have been introduced into the gut microbiome.  (Pimentel 60)

It’s probably safe to say that we all suffer from digestive distress at some point in our lives, but some of us have on-going and very difficult struggles with IBS - “Irritable Bowel Syndrome”.  Irritable Bowel is an umbrella term that encompasses the entire digestive system, not just the colon.  The term “syndrome” implies that it’s not a disease when in fact, it is a disease and can be very serious and severe.  In the U.S., an estimated ten to fifteen percent of the population has IBS.  (Pimentel 18)  The definition of IBS is “any of the following symptoms for 3+ months:  abdominal pain and/or discomfort, diarrhea, constipation, bloating, gas, urgency, incomplete evacuation, relief or worsening of pain with defecation, brain fog, early satiety (a sense of fullness without having eaten much) or both diarrhea and constipation.”  (Pimentel 22)  

There are many reasons for IBS that include lactose intolerance, parasites, microscopic colitis, celiac disease, ulcerative colitis, and Crohn’s disease.  

What doesn’t cause IBS?  Anxiety or stress, but IBS can certainly cause stress and give you anxiety.

Three types of IBS

1. IBS-C = Irritable Bowel Syndrome with constipation.  This is found in 35% of patients.

2. IBS-D - IBS with diarrhea.  This is found in 40 percent of patients.  It’s important to rule out Crohn’s disease, ulcerative colitis, and celiac disease.

* Rifaximin is now FDA approved for treating IBS-D.

3. IBS-M IBS mixed type - alternating bouts of constipation and diarrhea.  This is found in 23% of patients.  

Identifying the root cause(s) of your IBS

This requires your practitioner to consider the entire digestive system - the function of each organ along the way.  The process of digestion is not just about breaking down food and turning it into waste.  It’s far more complex, and here are a few examples of digestive dysfunction that can lead to IBS. 

Pancreatic insufficiency - this occurs when the pancreas doesn’t produce enough digestive enzyme to break down food in the intestines and this may be directly related to the strength of the stomach acid.  

To note:  a lack of the fat enzyme lipase can also cause diarrhea and greasy, oily stool.  The chief complaint is significant abdominal pain.

Gallbladder - If your gallbladder has been removed or is not functioning properly, bile will flow straight from the liver into the small intestine and eventually to the colon, often resulting in diarrhea.  

It’s important to note that when bacteria encounter bile, they convert it to toxic bile acids (such as deoxycholic acid and lithocholic acid) which are believed to cause diarrhea.  This is known as bile acid diarrhea (BAD) and is different from SIBO, but it’s worse when SIBO is present. One of the main causes of BAD is SIBO.

Gut motility -  Digestion requires constant, synchronized contractions of the various gut muscles to control the movement of food through the GI tract - this is known as gut motility.  Abnormal gut motility can lead to pain, bloating, nausea, diarrhea, or constipation.    Generally speaking, if you suffer from IBS-C, your intestinal movements may be too slow, and if you have IBS-D, your gut may propel its contents too fast.  This is not a universal rule, however.  If your bowels are extremely slow, you may have diarrhea, and if they are fast, but not coordinated properly, this may lead to constipation.  

SIBO and IBS are separate medical conditions, but they commonly coexist, can be connected, and share similar symptoms. In fact, approximately 80% of IBS patients also have SIBO. In some cases, SIBO is a result of IBS, but in other cases, it’s not. 

Clinicians often use a breath test to diagnose SIBO and an antibody blood test to diagnose IBS.  It’s common for a patient to take both clinical tests together when diagnosing their GI symptoms. 


SIBO, or small intestinal bacterial overgrowth, is defined as the presence of excessive numbers of bacteria in the small bowel, causing gastrointestinal symptoms.  The normal small bowel has lower levels of microbial colonization than does the colon. This normal balance is significantly disrupted with SIBO.  

SIBO can be a complex result of various medications and conditions such as IBS, Celiac, Crohn’s disease, bowel surgeries, and other gastrointestinal complications. The symptoms of SIBO can arise from the malabsorption of nutrients, alteration in intestinal permeability, inflammation, and/or immune activation that arises from the abnormal bacterial fermentation within the small bowel.  SIBO symptoms can include any combination of the following:  a flat belly upon waking, and bloating begins after eating and gets worse throughout the day, nausea, constipation, diarrhea, gas, acid reflux, and alternating constipation and diarrhea, brain fog,  multiple food intolerances, reactions to high FODMAP foods, feel worse if you take probiotics or eat probiotic rich foods, or your digestive issues improve when you take antibiotics. 


The three primary fermented gasses in the microbiome are hydrogen, methane, and hydrogen sulfide and they are not independent of each other.  In fact, these gasses interact with each other in a complex way. Hydrogen is produced by fermenting bacteria but is also consumed by other organisms, resulting in the production of other gasses including methane and hydrogen sulfide. 


1. Methane  = CONSTIPATION 

Elevated levels of methane are indicative of IMO.  IMO, or intestinal methanogenic overgrowth, is an overgrowth of methane-producing archaea in the small and large intestines. Methanogens are not bacteria (the “B” in SIBO) but are archaea and may also overgrow in the colon and not just the small intestine (the “SI'' in SIBO).  In humans, excess methane production appears to be caused by Methanobrevibacter smithii, which is the predominant methanogen in the human gut. Research has indicated a link between obesity and methane-producing archaea due to the fact that the longer food stays in the gut, the more calories are absorbed each time you eat. 

2. Hydrogen  = BLOATING 

The two main “weeds” in SIBO are E. coli and Klebsiella and are hydrogen producers which leads to bloating.  These bacteria are very disruptive to the small intestine and bully the other bacteria to the point that they die off.

3. Hydrogen Sulfide = GAS

Excess hydrogen sulfide is a condition in which sulfate-reducing organisms produce high amounts of hydrogen sulfide in the gut. Excess hydrogen sulfide was undetectable by traditional breath testing prior to trio-smart, and patients with excess hydrogen sulfide may have appeared "normal" on previous breath tests. 


Excess hydrogen sulfide is associated with diarrhea.  Hydrogen sulfide SIBO is much more common in those with inflammatory bowel disease such as Crohn’s disease or ulcerative colitis. People with hydrogen sulfide SIBO do not tolerate high sulfur foods well. This includes garlic, onion, cabbage, broccoli, cauliflower, eggs, garlic, onion, among others. It is thought that people with hydrogen sulfide SIBO have difficulty metabolizing sulfur in their diet and their body puts more sulfur into their intestines.


1. Bacterial build up in the small intestine - ANY factor that slows down the speed of flow through the small intestine has the potential to cause overgrowth.

Blockages - tumors, polyps, kinks, adhesions .  Bypass weight loss surgery can lead to SIBO.

Motility issues - damage to the cleaning waves.  This can come from food poisoning, chronic untreated constipation (especially in children), and the subsequent development of anti-vinculin and anti-CdtB antibodies. 

Adhesions - complications from surgery, radication, tumors - can lead to the development of scarring inside the abdomen which can lead to SIBO. 

Endometriosis  - can lead to adhesions of the abdomen which affects gut motility and leads to bacterial overgrowth.  

Inflammatory diseases such as Crohn’s, Colitis, and Celiac can cause significant inflammation in the wall of the small intestine and inhibit bowel clearance.  They can also lead to strictures (abnormal narrowing) that can alter the gut as well.  

Diabetes - one of the most common diseases that affect gut motility.  One of the long-term consequences and most common complications of diabetes is peripheral neuropathy - nerve damage caused by chronically high blood sugar levels.  The nerve damage can affect the nerves in the gut as well.

Autoimmune diseases - various autoimmune diseases - such as scleroderma lupus erythematosus, and other connective tissue diseases can also cause poor gut motility.  

Drugs such as narcotics, anticholinergics.  Narcotics slow down the gut causing constipation, heartburn, and abdominal discomfort.  The opioid crisis has definitely led to an increase in SIBO cases.   Anticholinergics are used both in urology and gastroenterology to decrease the symptoms or urinary infrequency or abdominal cramps.  The action of this drug is to slow gut motility.

Most common cause = lack or impairment of the cleaning waves in the gut.  This happens every 90 - 120 minutes when you aren’t eating.  

Natural protective factors against SIBO

1. Stomach acid (HcL - Hydrochloric acid)

2. Antimicrobial effects of bile acid and pancreatic secretions

3. Phase III migrating motor complexes (housekeeper waves)

4. Ileocecal valve


1. GIMAP stool test- represents the microbial evidence of the colon (large intestine). 

The microbiome of the small intestine (the 20 feet of gut that precedes the colon) is radically different than the colon, and may be considered eminently more important than the microbiome in the stool.

  • Elevated levels of E. coli, Klebsiella and possibly Aeromonas in a stool test can predict a positive breath test and can produce hydrogen in the small bowel.  

  • Elevated levels of Methanobrevibacter smithii (which cause constipation and bloating) 

  • Elevated Fusobacterium, Desulfovibrio, and Bilphila which make hydrogen sulfide from hydrogen which is associated with diarrhea.

2. IBS Smart blood test.  Tests for CdtB - the active protein Cytolethal Distending Toxin.  When CdtB enters the bloodstream, antibodies are produced by the immune system to fight it.  Vinculin is an important protein that helps the gut muscles contract efficiently.  Their antibodies attack the vinculin, gut function is impaired which affects the cleaning waves.  

This test measures the specific antibodies to CdtB and vinculin in the blood and and that it’s a disease and that your diarrhea is not due to Crohn's, ulcerative colitis, or celiac.  This test is not useful for patients with IBS-C.

Price = $220. Along with your results, you will receive an itemized receipt (superbill) for use when filing an insurance claim. Ibs-smart is covered at least in part by many common insurance plans. If you're interested in asking your insurance provider about coverage, you can reference PLA code: 0164U. 

NOTE:  Medicare and Medicaid may not cover online services.

3. Trio-Smart SIBO breath test

The trio-smart breath test is applicable to patients who experience bloating, gas, abdominal pain, constipation and/or diarrhea.  This test measures the levels of hydrogen, methane, and hydrogen sulfide in your breath. Elevated levels of gases can indicate small intestinal bacterial overgrowth (SIBO), intestinal methanogenic overgrowth (IMO), and/or excess hydrogen sulfide.


Price = $349.  Along with your results, you will receive an itemized receipt (superbill) for use when filing an insurance claim. Trio-smart is covered at least in part by many common insurance plans. If you're interested in asking your insurance provider about coverage, you can reference CPT code: 91065 (billed twice).

​NOTE:  TrioSmart contacts your insurance, and to date, all of my patients who have completed the SIBO breath test have Regence insurance which paid 100% of the test.


1. Identify the cause of SIBO 

2. Treat the SIBO

A. Methane

Antibiotics don’t work as well because methanogens are from the kingdom archaea, and they are not bacteria.  However, a combination of rifaximin and neomycin is effective. The main challenge with antibiotics is that methane seems to relapse sooner and more often. 

Lovastatin blocks an enzyme within the methane producing microorganism.

Better options include supplements such as oil of oregano, garlic extract (allicin).

B. Hydrogen (IBS-D) 

Rifaximin is FDA approved to treat IBS with diarrhea

C. Hydrogen Sulfide

Rifaximin + Bismuth inhibits hydrogen sulfide production.  

3. Diet, medications and supplements to maintain control and prevent recurrence of SIBO

A. Diet


1. Dairy due to lactase deficiency.

Most with IBS and SIBO do not tolerate dairy and experience bloating, pain, diarrhea, discomfort, etc. because after a bout of food poisoning, the villi (small finger-like projections that increase the surface area of the small intestine) are damaged by the infection.  When the villi grow back, they don’t necessarily produce the same quantity of enzymes including lactase (which is needed to digest lactose, the sugar in dairy).

2. Gluten -   foods containing gluten are highly fermentable.  You may be able to tolerate gluten after you resolve your IBS/SIBO. 

3. Inulin - food additive and a prebiotic.  Extracted from chicory root fiber.  Also found in  asparagus, garlic, and bananas.  

4. Artificial sweeteners - except aspartame.  It’s considered a peptide rather than a sugar.  

5. Low-fermentation diet- restrict products that contain high levels of carbohydrates or ingredients in food that humans can’t digest, and therefore are digested by bacteria

6. Timing your eating - space your meals out 4 - 5 hours between so that the housekeeping wave cycles have a chance to work their magic.  

Two states of digestion:

A. Fasting state - aka “cleaning” mode

B. Feeding state - aka “grinding and digesting” mode

If you would like to learn more about this topic, I highly recommend Dr. Pimentel and Dr. Rezaie's book: The Microbiome Connection. Your Guide to IBS, SIBO, and Low-Fermentation Eating. I would consider this a must-have resource for anyone who suffers from IBS or SIBO, or who wants to better understand their microbiome.

As you can see, there are many factors and angles to addressing and resolving your GI distress, but functional nutritional therapy practitioners can help you from start to finish. If this article piqued your interest in taking care of your gut drama, I'd love to hear from you and help you.

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