What Is SIBO, and How It Could Be Causing Your IBS
By Dr Kelly Price
What Is SIBO (Small Intestinal Bacterial Overgrowth)?
SIBO or small intestinal bacterial overgrowth, is an accumulation and overgrowth of normal gastrointestinal (GI) bacteria in the small intestine. Normal bacterial counts in the small intestine are around 10^3 bacteria/mL, compared to 10^12 bacteria/mL in the large intestine. The small intestine is where most of our food is further digested and vital nutrients are absorbed. This overgrowth of bacteria competes for nutrients, interferes with digestion, and damages tissue.
SIBO Symptoms and the IBS Connection
The most common presentation of SIBO is a cluster of symptoms that overlap significantly with Irritable Bowel Syndrome (IBS), including excessive gas, bloating, constipation, diarrhea, or an alternating pattern between the two.
Beyond these digestive complaints, patients frequently experience acid reflux, nausea due to delayed gastric emptying, brain fog, fatigue, and heightened food sensitivities.
These food reactions are particularly pronounced with carbohydrates high in FODMAPs, an acronym for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols. These short-chain carbohydrates and sugar alcohols are poorly absorbed in the small intestine, so when they reach the colon and ferment, they draw in water and produce gas, leading to distension, discomfort, and abdominal pain.
SIBO and Leaky Gut: How the Two Are Connected
You may have heard the term "leaky gut," and it is closely tied to SIBO. In SIBO, the overgrown bacteria release toxins and metabolic byproducts that directly break down the tight junction proteins holding the intestinal lining together. This damage, compounded by the resulting inflammation and immune response, increases intestinal permeability, meaning the gut barrier becomes abnormally porous.
As a result, larger, undigested food particles and bacterial endotoxins can slip through the compromised lining into the bloodstream, triggering widespread, low-grade systemic inflammation. This "leaky gut" state then contributes to food sensitivities and other systemic reactions to foods. Importantly, these are typically delayed IgG/IgA-mediated responses, which differ fundamentally from true food allergies. True allergies involve IgE antibodies, which trigger rapid histamine release and can cause immediate, potentially life-threatening symptoms like hives, swelling, or anaphylaxis.
SIBO and Nutrient Malabsorption
The damage caused by SIBO also leads to malabsorption of essential vitamins, carbohydrates, proteins, and fats. If you have unexplained iron deficiency anemia, low vitamin B12, fatty or greasy stools (steatorrhea), bile acid malabsorption (which can cause explosive, watery diarrhea), or low serum albumin (a blood protein), SIBO may be the underlying culprit.
Conditions SIBO Is A Risk Factor For
IBS (60-80% is caused by SIBO)
Lactose Intolerance
Fructose Malabsorption
Sucrose Malabsorption
Malabsorption Syndrome
Dyspepsia
Leaky Gut
Anxiety (& Depression)
Mast Cell Activation Syndrome
GERD
Gallstone Disease
Sub-clinical atherosclerosis
Anemia (Fe/B12) or low ferritin
Omega 3 deficiency
Vit D deficiency
Hepatic Encephalopathy/Cirrhosis
NAFLD/NASH, Liver Inflammation
Carcinoma: pancreatic & cholangio
Conditions That Co-Exist With SIBO
Psoriasis
Restless Leg Syndrome
Rheumatoid Arthritis
Rosacea
Chronic Fatigue Syndrome/Fibromyalgia/Myalgic Encephalitis
Celiac Disease
IBD (Crohn's, Ulcerative Colitis)
Acne
Autism (31%)
Deep Vein Thrombosis
Obesity
Pancreatitis
Prostatitis (chronic)
Spina Bifida
Interstitial Cystitis
The Three Types of SIBO: Hydrogen, Methane, and Hydrogen Sulfide
There are three main types of SIBO, classified by the predominant gas produced by the overgrown organisms: hydrogen-dominant, methane-dominant, and hydrogen sulfide-dominant.
Hydrogen-producing bacteria, such as E. coli, Klebsiella, and Aeromonas, typically drive rapid intestinal transit and are most often associated with diarrhea.
Methane production is driven not by bacteria but by archaea, specifically Methanobrevibacter smithii, which slows gut motility and is strongly linked to constipation.
Hydrogen sulfide-producing bacteria, including Desulfovibrio and Fusobacterium varium, are less common and can present with a mixed symptom profile, causing either diarrhea, constipation, or an alternating pattern.
What Causes SIBO?
There is no single cause of SIBO and in most cases, it is multifactorial.
Migrating Motor Complex (MMC) Dysfunction
The most common underlying issue is a malfunction of the migrating motor complex (MMC), the "cleaning wave" that sweeps bacteria and cellular waste out of the small intestine between meals. MMC dysfunction can be triggered by stress, anxiety, grazing between meals, or even the sight or smell of food. Other contributors include hypothyroidism, Parkinson's disease, hEDS/POTS, diabetes, and Lyme disease. Certain medications such as opiates and antibiotics, as well as nerve injury can also impair MMC function.
Food Poisoning and Post-Infectious IBS
Food poisoning is another major cause, often leading to what we call post-infectious IBS. In this scenario, the immune system mistakenly produces antibodies against a protein on the gut's nerve cells. This nerve damage impairs motility, and as a result, this very common form of SIBO can be difficult to treat unless we address and calm the underlying autoimmune reaction.
Structural Causes of SIBO
Structural causes of SIBO occur when the physical anatomy of the digestive tract is altered, creating pockets where bacteria can pool or bypassing natural barriers that normally keep bacterial counts low in the small intestine. Common examples include small intestinal diverticula (outpouchings in the intestinal wall), surgical adhesions, strictures from Crohn's disease, and gastric bypass surgery, all of which can create stagnant areas where food and bacteria accumulate instead of being swept forward.
Additionally, removal or dysfunction of the ileocecal valve, the sphincter that separates the small intestine from the bacteria-rich large intestine, can allow colonic bacteria to reflux backward into the ileum. Even prior abdominal or pelvic surgeries that cause scar tissue can kink or narrow the bowel, mechanically slowing transit and creating a breeding ground for overgrowth. Unlike motility or immune-related causes, structural issues are often permanent and may require surgical correction, though antibiotics and prokinetics are still used to manage the resulting bacterial overgrowth.
Low Stomach Acid, Bile, and Digestive Enzymes
Stomach acid, bile acids, and digestive enzymes do more than break down your food. They also act as natural germ-fighters that keep bacteria from overgrowing in your small intestine. Stomach acid is your first line of defense. It kills most bacteria that enter with your meals. When acid levels are low, whether from acid-blocking medications, aging, or other conditions, more bacteria survive and make their way into the small intestine.
Bile acids, which are released from your liver, have their own bacteria-fighting properties. They help disrupt bacterial cell membranes. When bile flow is sluggish or deficient, bacteria can take hold and multiply. Pancreatic enzymes help by breaking down carbohydrates and proteins that bacteria would otherwise feed on. They can also directly damage bacterial cell walls. When any of these digestive secretions are lacking, whether from pancreatic issues, liver disease, or gallbladder removal, your small intestine loses its natural protection. This makes it easier for bacteria to overgrow, which can lead to or worsen SIBO.
How Is SIBO Diagnosed? The Lactulose Breath Test
Diagnosis of SIBO is done by measuring the exhaled gases produced by the bacteria. This test is referred to as a lactulose breath test. Lactulose is a synthetic sugar that is poorly absorbed by the GI and readily fermented by SIBO bacteria.
By starving the GI of FODMAPs and other fuel for 1-2 days then drinking a lactulose solution, we can measure the levels of gas produced at 15-20 minute intervals over a 2-3 hour period. Depending on which gases are produced, their levels and the time they are produced, we can determine what kind of SIBO a patient might have.
How We Help With SIBO at Terrain Natural Medicine
At Terrain Natural Medicine, we take a root-cause approach to SIBO that goes beyond just treating symptoms. If you suspect SIBO is behind your digestive issues, we start with a thorough health review and non-invasive breath testing to confirm the diagnosis and pinpoint which type of gas is causing your symptoms, so we can create a plan tailored to you.
Your personalized protocol may include natural antimicrobials, and targeted nutrients to repair intestinal damage. We also address the underlying reasons SIBO started in the first place. We see you as a whole person, not just a gut. That's why we also support your immune system, help you manage stress, and guide you through a careful reintroduction of foods to prevent relapse. We can walk with you every step of the way, with education, regular check-ins, and gentle adjustments, so you can heal sustainably and feel like yourself again.
If your gut has been running the show, we'd love to help you understand why and gently guide you back to feeling like yourself again.
