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16S rRNA Gene Sequencing from Stool for Bacterial Identification

Published: August 9, 2026Updated: August 16, 2026

This test analyzes genetic material from bacteria in your stool to identify specific bacterial species. It helps determine if certain bacteria are present that may be causing an infection.

Quick summary

["This test helps doctors diagnose infections linked to harmful bacteria in your digestive system."]

Medically reviewed by WellAlly Editorial TeamLast reviewed August 16, 2026Editorial policy

Key facts at a glance

LOINC
94603-8
Short code
16SSEQ
Synonyms
Bact 16S rRNA gene Islt-Seq
Category
chemistry
Sample
serum
Container
Sterile, leak-proof container appropriate for clinical isolate submission (e.g., cryovial, sterile screw-cap tube) or appropriate transport medium (e.g., Amies or Stuart transport medium for swab specimens, blood culture bottles for blood specimens)
Units
N/A
Fasting
false
Population
adult
Sex
all
Age range
18–65 years
Method
sequencing
CPT
87153
SNOMED
397428000
Specimen volume
Variable depending on specimen type; minimum 1 mL for liquid specimens (blood, body fluids) or visible bacterial growth on solid medium for isolate submissions. Pure culture isolate is preferred over mixed cultures.
Stability
Isolates: stable at 2-8°C for up to 7 days for short-term storage; indefinite storage at -70°C or below in appropriate cryopreservation medium (e.g., tryptic soy broth with 15-20% glycerol). DNA extracts: stable at 2-8°C for up to 30 days or at -20°C or below for long-term storage. Whole blood/blood culture bottles: follow blood culture protocol; transport at room temperature.
Hemolysis max
500
Lipemia max
1000
Icterus max
500
TAT
48–168 hours
Order
routine

What This Test Measures

The test looks for unique genetic sequences (16S rRNA) from bacteria found in your stool. These sequences act like a molecular fingerprint, allowing doctors to identify which bacteria may be present.

How the Test Works

A small sample of your stool is collected and processed to extract bacterial DNA. Specialized lab equipment then sequences this DNA to compare it against known bacterial genetic databases.

When You Might Need This Test

Your doctor may recommend this test if you have symptoms like persistent diarrhea, unexplained weight loss, or if you’ve been exposed to bacteria that cause gastrointestinal infections.

Common Uses

This test is often used to diagnose infections caused by bacteria like *Escherichia coli*, *Salmonella*, or other pathogens that may not be detected by traditional stool cultures.

Reference range

Results reported as identified bacterial genus and species based on sequence homology comparison to validated 16S rRNA gene databases (e.g., NCBI GenBank, RIDOM, SmartGene). Identification confidence reported as percent identity match. No reference range applies; result is qualitative presence/absence with species-level identification when match criteria are met (typically ≥97% identity for genus and ≥99% identity for species).N/A

Specimen: serum

No special patient preparation required. Specimen should be collected prior to initiation of antimicrobial therapy whenever possible to maximize pathogen recovery. For blood cultures, collection should be performed using strict aseptic technique to avoid contamination with skin flora.

Clinical interpretation

How abnormal results are interpreted and what conditions they suggest.

◆Associated findings1

Short name

Stool Bacterial DNA Sequencing

Frequently asked questions

Why might my doctor order this test?
Your doctor may order this test if they suspect a bacterial infection in your digestive system, especially if standard tests like stool cultures haven’t provided clear results or if symptoms persist.
How long does it take to get results?
Results can take several days to a couple of weeks, depending on lab processing times and database comparisons. Your doctor will discuss the findings with you once available.
Is there any preparation needed before the test?
No special preparation is required, but you may be asked to avoid certain medications (like antibiotics) that could affect bacterial counts in your stool for a few days before testing.
  1. 1
    MedlinePlus — Laboratory TestsSource
  2. 2
    Lab Tests OnlineSource
  3. 3
    Mayo Clinic — Tests & ProceduresSource

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.

Medical Disclaimer

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