What causes foul-smelling stool after a colonoscopy?

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Last updated: April 23, 2025View editorial policy

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From the Research

Odorous stool after a colonoscopy is a common and typically temporary side effect that can be managed with probiotics, as evidenced by a study published in 2018 1, which found that probiotic administration can reduce symptoms of irritable bowel syndrome, including stool consistency and frequency, gas, abdominal pain, and flatulence. This occurs primarily due to the bowel preparation process before the procedure, which disrupts your normal gut bacteria balance. The cleansing solutions flush out both harmful and beneficial bacteria, allowing different microorganisms to temporarily dominate your digestive system, resulting in changes to stool odor. Some key points to consider:

  • The bowel preparation process can cause changes in stool odor due to the disruption of the gut microbiome.
  • Probiotics can help restore the balance of the gut microbiome and reduce symptoms of irritable bowel syndrome, as shown in a study published in 2017 2, which found that patients who took probiotics after colonoscopy had a lower number of pain days compared to those who took a placebo.
  • Staying well-hydrated and gradually returning to a normal diet can also help alleviate symptoms.
  • If the unusual odor persists beyond a week, is accompanied by severe abdominal pain, fever, or bloody stools, it is essential to contact a healthcare provider, as these could indicate complications such as infection. It is also worth noting that a study published in 2022 3 found that antibiotics can differentially affect the gut microbiota in different segments of the gut, which could have implications for the management of odorous stool after colonoscopy. However, the use of antibiotics is not typically recommended for this condition, and probiotics are generally considered a safer and more effective option.

Professional Medical Disclaimer

This information is intended for healthcare professionals. Any medical decision-making should rely on clinical judgment and independently verified information. The content provided herein does not replace professional discretion and should be considered supplementary to established clinical guidelines. Healthcare providers should verify all information against primary literature and current practice standards before application in patient care. Dr.Oracle assumes no liability for clinical decisions based on this content.

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