Colonoscopy with Stool Microbiome Analysis (16S rRNA Gene Sequencing)
This test examines the bacteria present in your stool to help assess gut health, identify potential infections, or evaluate changes in your microbiome after procedures like a colonoscopy.
["Understanding your gut’s bacterial balance can help guide treatment for digestive issues or infections."]
Key facts at a glance
- LOINC
- 28033-9
- Short code
- Colonoscopy study thru stoma
- Synonyms
- Colonoscopy study thru stoma
- Category
- chemistry
- Sample
- serum
- Container
- Red-top tube (SST)
- Units
- N/A
- Fasting
- false
- Population
- adult
- Sex
- all
- Age range
- 18–65 years
- Method
- colonoscopy
- Specimen volume
- 5 mL
- Stability
- Room temperature: 4h, Refrigerated: 24h, Frozen: 7d
- Hemolysis max
- 500
- Lipemia max
- 1000
- Icterus max
- 500
- TAT
- 4–24 hours
- Order
- routine
Why This Test Might Be Ordered
Your healthcare provider may recommend this test if you have symptoms like persistent diarrhea, unexplained weight loss, abdominal pain, or if you’ve had a recent colonoscopy to check for changes in your gut bacteria. It can also help monitor conditions like inflammatory bowel disease (IBD) or infections like Clostridioides difficile.
What to Expect Before the Test
You’ll likely need to prepare by avoiding certain foods or medications for a few days before the test. Your provider may also instruct you to follow a special diet or take a laxative to ensure a clean sample. Bowel prep is standard for colonoscopy procedures.
During the Procedure
The test involves collecting a small sample of stool during or after your colonoscopy. The sample is then analyzed to identify and quantify different types of bacteria in your gut microbiome. This process helps determine if there are imbalances or infections present.
What the Results Mean
Results show the relative abundance of various bacterial species. Abnormal patterns may indicate infections, overgrowth of harmful bacteria, or shifts in gut health. Your provider will interpret these findings in the context of your symptoms and medical history.
Clinical interpretation
How abnormal results are interpreted and what conditions they suggest.
◆Associated findings1
Short name
Stool Microbiome Test
Frequently asked questions
Your microbiome plays a key role in digestion, immune function, and overall health. Changes in bacterial balance can signal infections, inflammation, or other gastrointestinal issues. This test helps healthcare providers tailor treatments, such as antibiotics or probiotics, to restore balance.
How long does it take to get results? Results are typically available within 1–2 weeks after the sample is collected, depending on lab processing times.
Is this test covered by insurance? Coverage depends on your insurance plan and the reason for testing. Check with your provider or insurance company to confirm coverage details.
Sources
- 1
- 2Lab Tests OnlineSource
- 3
Click any link to access the full source. PubMed Central (PMC) links provide free full-text access.
This information is for educational purposes only and is not a substitute for professional medical advice, diagnosis, or treatment.
This content is for general informational and educational purposes only and is not a substitute for professional medical advice, diagnosis, or treatment. Always seek the guidance of a qualified healthcare provider with any questions you have about a medical condition, and never disregard professional medical advice or delay seeking it because of something you read here.
If you think you may have a medical emergency, call your local emergency number or go to the nearest emergency department immediately.
Medically reviewed by WellAlly Editorial Team Last reviewed August 16, 2026. · Read our editorial policy