When Bacteria Go Where They Don’t Belong
(Small Intestinal Bacterial Overgrowth)
The gut is home to trillions of bacteria—many of which are beneficial and essential for health. But when too many bacteria migrate into the wrong part of the digestive system, it can create a cascade of symptoms that are frustrating, chronic, and often misdiagnosed. This is called Small Intestinal Bacterial Overgrowth, or SIBO.
What Is SIBO?
SIBO occurs when there is an abnormal increase in the overall bacterial population in the small intestine, especially types of bacteria that are typically found in the large intestine. The small intestine is designed for nutrient absorption, not heavy fermentation. When bacteria overpopulate this space, they ferment the food you eat too early, producing gas and inflammation—and leaving you with pain, bloating, and misery.
Symptoms of SIBO
- Chronic bloating
- Abdominal pain or discomfort
- Nausea
- Belching, excessive burping
- Feeling uncomfortably full after meals
- Heartburn or reflux
- Diarrhea, constipation, or alternating between both
- Fatigue, nutrient deficiencies, or unintended weight changes
SIBO symptoms are often mistaken for IBS, food intolerances, or “just stress.” (https://my.clevelandclinic.org/health/diseases/21820-small-intestinal-bacterial-overgrowth-sibo)
Why People with Endometriosis Are at Higher Risk
SIBO doesn’t happen in isolation—it often develops in response to disruption in how food moves through the gut (https://pmc.ncbi.nlm.nih.gov/articles/PMC5859071/). For people with endometriosis, that disruption can come from multiple angles:
Surgery
Abdominal or pelvic surgeries (including endometriosis excision) can:
- Slow food transit time through the gut
- Cause nerve disruption or inflammation
- Involve manipulation of organs, which can alter the gut microbiome
Adhesions
Adhesions—bands of internal scar tissue—are common in endometriosis and after surgery. They can:
- Tether and kink the small intestine, disrupting normal flow
- Trap bacteria or create areas of stasis, ideal for overgrowth
- Lead to chronic GI symptoms that persist even after excision
Hormonal and Immune Changes
Endometriosis itself creates an inflammatory environment that can change gut motility, immune function, and the gut lining—further tipping the scales in favor of SIBO.
Types of SIBO
There isn’t just one kind of SIBO—and the type of gas produced by the bacteria helps determine your symptoms and treatment.
- Hydrogen-dominant SIBO
- More likely to cause diarrhea
- Associated with bloating and cramping
- Diagnosed via hydrogen breath testing
- Methane-dominant SIBO (now called IMO, Intestinal Methanogen Overgrowth)
- Often linked with constipation, gas, and bloating
- Caused by archaea (methane-producing microbes)
- Harder to treat, more stubborn recurrence
- Hydrogen Sulfide SIBO
- Less common and harder to diagnose
- Symptoms may include rotten egg-smelling gas, fatigue, and neurological symptoms
- Standard breath tests may miss it
How Is SIBO Diagnosed?
Breath Testing
The gold standard is a lactulose or glucose breath test, where hydrogen and methane gases are measured after ingesting a sugar substrate.
Symptom tracking
Some clinicians also diagnose based on history and symptoms, especially when breath testing is inaccessible or inconclusive.
How Is SIBO Treated?
SIBO treatment is often a multi-phase approach
- Antimicrobials
- Prescription antibiotics like rifaximin (for hydrogen) or rifaximin + neomycin (for methane)
- Or herbal antimicrobials like berberine, oregano oil, allicin (often used with functional medicine providers)
- Dietary changes
- Many use a low-FODMAP, SIBO-specific, or elemental diet to reduce fermentation
- Note: diet alone won’t eradicate SIBO but may reduce symptoms
- Motility support (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030608/)
- After treatment, prokinetics (like low-dose erythromycin or herbal blends) help prevent relapse by keeping food—and bacteria—moving
- Especially important for people with slowed gut motility from adhesions or nerve dysfunction
- Address the root cause
- Adhesions, endometriosis, gut-brain axis issues, vagus nerve tone—all of these matter
- If you don’t address why the overgrowth happened, it’s likely to come back
How Are SIBO and Endometriosis Connected?
SIBO and endometriosis are frequent companions—and not by coincidence. While they affect different systems, they both disrupt the gut, immune function, and the body’s ability to regulate inflammation and motility.
Here’s how they intersect:
1. Slowed Gut Motility
Endometriosis—especially deep infiltrating or pelvic disease—can impair how food moves through the intestines. Pain, inflammation, and nerve disruption from endometriosis (or surgery for it) can lead to intestinal stasis, giving bacteria time to overgrow in the small intestine.
2. Adhesions
Endometriosis can cause adhesions, and so can excision surgery. These adhesions may tether or kink the small intestine, creating pockets of slowed transit or structural narrowing—ideal environments for bacterial buildup.
3. Chronic Inflammation
Both conditions trigger systemic inflammation. Endometriosis promotes inflammatory cytokines that affect gut lining integrity, while SIBO worsens inflammation by releasing bacterial byproducts that can further sensitize the nervous system and increase gut permeability.
4. Immune Dysregulation
Many with endometriosis experience immune dysfunction—overactive in some places, underactive in others. This dysregulation can impair the gut’s ability to keep microbial populations in balance, allowing overgrowth in the small intestine to take hold.
5. Misdiagnosis & Diagnostic Delays
SIBO and endometriosis share overlapping symptoms: bloating, pain, nausea, bowel changes. Many patients are told they have “just IBS” or are given dietary advice without evaluation for either root cause. Both conditions are underdiagnosed and misunderstood, leading to prolonged suffering.
In short:
Endometriosis disrupts the gut. SIBO thrives in that disruption.
Could SIBO Be Why You Still Feel Sick After Excision?
If you’ve had endometriosis excision but are still bloated, still nauseous, still living on ginger tea and hope—SIBO may be the missing piece.
It’s not “just stress.” It’s not “normal post-op healing.”
It’s not “just IBS.”
It’s something we can test. Something we can treat.
At ESSI, We Don’t Just Excise—We Investigate.
At ESSI, we evaluate the whole picture. If SIBO is suspected, we coordinate testing, explore the gut-pelvis connection, and collaborate with providers who understand what it’s like to live in a body that doesn’t follow textbook rules.
Bloating is complex-you deserve answers.
