DR. THOMAS BACHARACH

Specialist in General Medicine

🕑 Reading time: 3–5 minutes

👆 Key takeaways

• SIBO (small intestinal bacterial overgrowth) describes an excessive bacterial overgrowth in the small intestine—often with symptoms that resemble IBS (bloating/distension, abdominal pain, diarrhea/constipation).
• A colonoscopy is generally not considered a direct cause of SIBO. In most cases, chronic factors such as motility disorders, low stomach acid, or anatomical changes are involved.
• In theory, bowel prep, medications/sedation, and pre-existing risk factors can temporarily stress the system—so if new symptoms appear after a colonoscopy, breath-test diagnostics may be useful.

Can a Colonoscopy Cause SIBO?

1. What is SIBO?
2. What causes SIBO?
3. Can a colonoscopy cause SIBO?
4. Colonoscopy for diagnosing SIBO?
5. What to do if symptoms occur after a colonoscopy?
6. Summary
7. FAQs
8. References

1. What is SIBO?

SIBO stands for “Small Intestinal Bacterial Overgrowth”, meaning an abnormal bacterial overgrowth in the small intestine.

In a healthy gut, most bacteria are located in the colon, while the small intestine contains comparatively few bacteria.
With SIBO, however, colon-type bacteria migrate into the small intestine and multiply excessively—often described as roughly
100,000 bacteria per milliliter of small-intestinal fluid.

Typical symptoms (often IBS-like, which is why SIBO is frequently mistaken for irritable bowel syndrome):

• Severe bloating and a visibly distended abdomen, especially after meals
• Abdominal pain, fullness, belching
• Diarrhea,
  constipation,
  or alternating bowel habits
• Fatigue, weight loss, or nutrient deficiencies (e.g., vitamin B12) in long-standing SIBO

SIBO is therefore often recognized only after typical IBS strategies do not help sufficiently and targeted
diagnostics (e.g., a breath test) are performed.

Exhausted, tired, “brain fog”—and your gut is acting up?

For many people, bloating, abdominal pain, and bowel changes are caused by small intestinal bacterial overgrowth (SIBO).

Dr. Thomas Bacharach shares his knowledge to explain how SIBO can affect the whole body—and what next steps may be helpful.

Learn more

2. What causes SIBO?

SIBO typically does not appear “out of nowhere,” but rather results from impaired natural defense and cleansing mechanisms in the upper gut.
Key causes and risk factors include:

• Slowed intestinal motility:
  In diabetes, Parkinson’s disease, scleroderma, chronic IBS, or with certain medications, food moves more slowly through the small intestine—giving bacteria more time to settle and multiply.
• Reduced stomach acid production:
  Proton pump inhibitors (PPIs), chronic gastritis, or increasing age can reduce stomach acid, which normally helps kill bacteria.
• Anatomical changes:
  Abdominal surgery, scar tissue, diverticula, stenoses, or a shortened small intestine can create “pockets” where bacteria stagnate.
• Ileocecal valve dysfunction:
  This valve between the small intestine and colon normally prevents backflow; if it fails, colonic bacteria can migrate into the small intestine.
• Digestive enzyme or bile acid deficiency:
  Pancreatic insufficiency or bile flow problems can impair digestion and promote bacterial overgrowth.

Additionally, antibiotics, immune suppression, chronic inflammation, or an altered gut microbiome can increase risk.

3. Can a colonoscopy cause SIBO?

Patients often wonder whether a colonoscopy could be the cause of their SIBO. Colonoscopy is not considered a direct cause of SIBO.
SIBO usually develops due to chronic factors (e.g., motility disorders, prior surgeries, medications, low stomach acid)—not because of a single endoscopic procedure.

That said, there are indirect mechanisms through which a colonoscopy could theoretically contribute—especially in people who are already predisposed:

• Bowel preparation:
  Intensive laxative prep can temporarily disrupt the gut microbiome and alter colonization patterns in the digestive tract.
• Sedation and medications:
  Sedatives or other drugs can slow intestinal motility, so food remains longer in the small intestine and bacteria have more time to proliferate.
• Pre-existing risk factors:
  People with IBS, diabetes, pancreatic issues, or those using acid blockers are generally more susceptible—so a colonoscopy may be an additional stressor rather than the actual trigger.

Important: There are no conclusive studies showing that a colonoscopy alone typically triggers SIBO.

4. Colonoscopy for diagnosing SIBO?

A colonoscopy is only of limited use for diagnosing SIBO itself, because SIBO refers to overgrowth in the small intestine, and this area is not reliably visualized in a standard colonoscopy.
However, endoscopy can be very helpful to rule out or identify other causes of symptoms (e.g., inflammation, signs suggestive of celiac disease on gastroscopy, polyps, tumors, bleeding sources) and to take biopsies—valuable in terms of differential diagnosis.

For SIBO, breath tests (e.g., lactulose or glucose) are commonly used in practice as non-invasive methods.
A frequently cited gold standard is the quantitative microbiological analysis of an endoscopically obtained small-intestinal aspirate, because it can directly quantify bacterial load in the small intestine. However, this approach is more invasive and resource-intensive. In routine practice, breath testing is therefore widely used.

5. What to do if symptoms occur after a colonoscopy?

If new or significantly worse symptoms such as bloating, fullness, diarrhea, or a distended abdomen occur after a colonoscopy, it’s sensible to proceed in a structured way—rather than automatically blaming the procedure.

• Document symptoms: When do symptoms start, what makes them better/worse (food, stress, medications)?
• Seek medical assessment: Especially if symptoms persist, worsen significantly, or markedly affect quality of life.
• Discuss SIBO diagnostics: A hydrogen/methane breath test is often the next reasonable step.
• Consider other causes: Intolerances, infections, IBS triggers, medication effects, or underlying motility issues.

Note: Alarm signs such as blood in the stool, fever, persistent vomiting, significant weight loss, or severe pain should always be evaluated promptly.

For information on treatment options for SIBO (e.g., rifaximin or other antibiotic agents) and nutrition for SIBO (e.g., reducing certain carbohydrates; low FODMAP), please see the linked articles.

6. Summary

A colonoscopy is generally not the cause of SIBO. If symptoms appear after the procedure, this may be related to temporary changes (e.g., bowel prep, medication effects) and underlying risk factors.
If symptoms persist, it can be worthwhile to discuss targeted testing (e.g., a breath test) with your physician to clarify the cause.

7. FAQs

8. References

1. 1. 1. 1. IMD Berlin. (n.d.). 372 Small intestinal bacterial overgrowth (SIBO).
            https://www.imd-berlin.de/fachinformationen/diagnostikinformationen/300-399/372-duenndarmfehlbesiedlung-sibo
            (Accessed on 26 Jan 2026)
         2. Gastroklinik CH. (n.d.). SIBO – Small intestinal overgrowth: cause and treatment.
            https://www.gastroklinik.ch/sibo-duenndarmueberwucherung/
            (Accessed on 26 Jan 2026)
         3. Medical Tribune. (n.d.). Overgrowth in the small intestine.
            https://www.medical-tribune.de/medizin-und-forschung/artikel/wucher-im-duenndarm
            (Accessed on 26 Jan 2026)
         4. Reizdarm-SOS. (n.d.). Possible causes of SIBO and IMO.
            https://www.reizdarm-sos.de/blogs/reizdarm-sos-blog/mogliche-ursachen-von-sibo-und-imo
            (Accessed on 26 Jan 2026)
         5. Premium Medical Circle. (n.d.). Recognizing & treating SIBO: symptoms, causes, treatment.
            https://premiummedicalcircle.com/de/artikel/sibo-wenn-bakterien-am-falschen-ort-die-ursache-fur-bisher-unerklarliche-beschwerden
            (Accessed on 26 Jan 2026)
         6. Madena. (n.d.). Small intestinal bacterial overgrowth (SIBO): symptoms, causes & diagnosis.
            https://madena.de/blogs/news/dunndarmfehlbesiedlung-sibo-symptome-ursachen-diagnose
            (Accessed on 26 Jan 2026)
         7. MSD Manuals. (n.d.). Small intestinal bacterial overgrowth (SIBO).
            https://www.msdmanuals.com/de/profi/gastrointestinale-erkrankungen/malabsorptionssyndrome/d%C3%BCnndarm-bakterien%C3%BCberwucherung-sibo
            (Accessed on 26 Jan 2026)
         8. Hoppe, G., & Fiedler, T. (2025). Bakterielle Dünndarmfehlbesiedlung (SIBO). Zeitschrift für Gastroenterologie. Thieme Connect.
            https://www.thieme-connect.de/products/ejournals/html/10.1055/a-2518-9266
            (Accessed on 26 Jan 2026)