SIBO (small intestinal bacterial overgrowth) isn’t caused by a single bacterium. It develops when bacteria that normally live in the large intestine migrate into or multiply within the small intestine, where bacterial populations are supposed to stay relatively low. The overgrowth typically involves a mix of species, and the specific types present determine which symptoms you experience and how the condition is treated.
Normal vs. Overgrown: What Changes
Your small intestine isn’t sterile, but it normally contains far fewer bacteria than your colon. SIBO is formally diagnosed when a sample from the small bowel contains 1,000 or more colony-forming units per milliliter, a threshold established in the American College of Gastroenterology’s clinical guidelines. Below that level, the bacteria present are considered a normal part of digestion. Above it, they start competing with your body for nutrients, producing excess gas, and damaging the intestinal lining.
The bacteria involved are mostly species that belong in the colon. They end up in the small intestine when the body’s normal defense mechanisms fail. Your digestive tract has a built-in cleaning cycle called the migrating motor complex, a pattern of muscular contractions that sweeps bacteria from the small intestine into the large intestine between meals and overnight. When this cycle is impaired, bacteria accumulate where they shouldn’t be. Structural issues play a role too. The ileocecal valve, which sits between the small and large intestine, acts as a one-way gate preventing colonic bacteria from flowing backward. Surgical removal of this valve or the formation of blind loops (dead-end pockets at surgical connection sites) can create persistent bacterial backflow and chronic SIBO.
The Three Types of Overgrowth
SIBO is now understood as three distinct subtypes based on which gas the overgrowing organisms produce: hydrogen, methane, or hydrogen sulfide. Each involves different microbes and tends to cause different symptoms.
Hydrogen-Dominant SIBO
This is the classic form of SIBO, driven by gram-negative bacteria like Escherichia coli and Klebsiella species, along with various anaerobes including Bacteroides fragilis. These bacteria ferment carbohydrates in the small intestine and release hydrogen gas, which causes bloating, abdominal pain, and often diarrhea. Gram-negative bacteria are particularly problematic because their outer membranes contain lipopolysaccharides (LPS), a toxic compound that is constantly released during bacterial division and cell death. When intestinal permeability increases, LPS can enter the bloodstream through gaps between intestinal cells, triggering the production of inflammatory signals like TNF-alpha and IL-6. This creates a cycle: inflammation damages the gut lining further, allowing more LPS through, which drives more inflammation.
Methane-Dominant Overgrowth (IMO)
Methane production in the gut comes not from bacteria but from archaea, a completely separate domain of life. The primary culprit is Methanobrevibacter smithii, the most well-studied methane-producing organism in the human gut. It feeds on the hydrogen gas that other bacteria produce, converting it into methane. Because these organisms aren’t technically bacteria, this subtype has been reclassified as Intestinal Methanogen Overgrowth, or IMO, rather than SIBO. All humans carry some population of these archaea, but problems arise when their numbers climb too high. When Methanobrevibacter smithii exceeds roughly 100 million organisms per gram in the gut, methane becomes detectable on breath tests.
Methane slows intestinal transit, so this subtype is strongly associated with constipation rather than diarrhea. There’s also growing evidence linking elevated methane-producing organisms to metabolic changes, with some research suggesting a role in obesity.
Hydrogen Sulfide SIBO
The third and most recently recognized subtype involves sulfate-reducing bacteria, primarily Desulfovibrio species, which account for roughly 66% of these organisms in the gut. A smaller proportion, about 16%, are Desulfobulbus species. These bacteria produce hydrogen sulfide gas, which at excessive levels damages the gut lining by interfering with how intestinal cells use butyrate, a key energy source for maintaining a healthy barrier. Breath hydrogen sulfide levels at or above 1.2 parts per million are considered clinically significant and correlate with diarrhea, urgency, and abdominal pain. Alterations in hydrogen sulfide levels have also been linked to inflammatory bowel conditions like ulcerative colitis and Crohn’s disease.
How These Bacteria Cause Symptoms
Regardless of which species dominate, the overgrowing bacteria cause problems through several shared mechanisms. One of the most important involves bile acids. Your liver produces bile acids to help you absorb dietary fat. Normally, about 95% of these acids are reabsorbed in the lower part of the small intestine and recycled back to the liver. The overgrowing bacteria produce an enzyme called bile salt hydrolase that strips bile acids of their chemical coating, a process called deconjugation. Once deconjugated, bile acids can no longer be reabsorbed by their normal transport system. Instead, they pass into the colon, where they stimulate fluid secretion and speed up motility, contributing to diarrhea.
Over time, this process depletes your total bile acid supply, making it harder to absorb fat and fat-soluble vitamins (A, D, E, and K). The bacteria also consume nutrients directly. Vitamin B12 deficiency is common in SIBO because the overgrowing bacteria use B12 for their own metabolism before your body can absorb it.
What Allows the Overgrowth to Happen
The bacteria involved in SIBO are normal residents of your digestive tract. The real question is what lets them end up in the wrong place or grow unchecked. Several factors lower the small intestine’s defenses.
- Impaired motility: Conditions that slow or disrupt the migrating motor complex, including diabetes, hypothyroidism, scleroderma, and post-infectious damage from food poisoning, allow bacteria to linger in the small intestine instead of being swept into the colon.
- Low stomach acid: Stomach acid kills many bacteria before they reach the small intestine. Long-term use of proton pump inhibitors (PPIs) reduces acid levels and has been associated with a moderately increased risk of SIBO, along with higher susceptibility to infections from Clostridium difficile, Salmonella, and Campylobacter.
- Structural abnormalities: Surgical removal of the ileocecal valve, intestinal strictures, adhesions from previous surgeries, and blind loops all create environments where bacteria can pool and multiply. Patients who have had ileocecal valve removal commonly report chronic bloating, gas, nausea, and diarrhea consistent with persistent SIBO.
- Immune deficiency: Conditions that weaken the gut’s local immune defenses, including IgA deficiency and immunosuppressive medications, reduce the body’s ability to keep bacterial populations in check.
How the Bacterial Type Is Identified
Breath testing is the most common way to determine which organisms are driving the overgrowth. After drinking a sugar solution (either glucose or lactulose), you breathe into a collection device at regular intervals. The gases detected, hydrogen, methane, or hydrogen sulfide, indicate which type of overgrowth is present.
These tests are far from perfect. A meta-analysis found the glucose breath test has a sensitivity of about 55% and specificity of 83%, meaning it correctly identifies SIBO just over half the time but is fairly reliable when it does come back positive. The lactulose breath test performs worse, with sensitivity around 42% and specificity of 71%. For hydrogen sulfide SIBO specifically, a rise to 25 parts per billion or higher, or a level at or above 62.5 parts per billion at the 90-minute mark, is considered a positive result.
The gold standard is a direct aspirate, where fluid is collected from the small intestine during an endoscopy and cultured to count bacterial colonies. This is more invasive and less commonly performed, but it provides the most definitive answer about which species are present and how numerous they are.