Fecal Sample Collection and Shipping SOP for Microbiome Analysis 


Mouse/Rat Fecal Sample Collection 

Following is the procedure for collection of murine fecal samples to be used for characterization of the fecal microbiota via 16S rRNA sequencing. 


• Sterile toothpicks.

• Autoclaved microisolator cages (completely empty).

• Sterile 1.5 mL Eppendorf tubes.


1. Pre-label Eppendorf tubes (one per mouse/rat). 

a. Sample ID (minimum).

b. Treatment group, if applicable.

c. Any other metadata you would like associated with the sample.

2. Place individual animal in empty autoclaved cage (no bedding). 

3. Allow mouse/rat to defecate normally and collect the first two fecal pellets per animal into an empty 1.5 mL Eppendorf tube using a sterile toothpick. Close tube securely. Discard toothpick after each animal. 

4. Place Eppendorf tube containing fecal pellets in -80°C freezer IMMEDIATELY

5. Maintain samples at -80°C until ready to ship. Samples may remain at -80°C for extended periods. 

6. Ship samples overnight with sufficient dry ice (2-3 day transport time) to ensure the samples stay frozen. 

Note: We recommend collection of all samples at the same time of day, preferably in the morning, as the microbiome content varies over the course of the day. 

Ship samples to:

IDEXX BioAnalytics

4011 Discovery Drive 
Columbia, MO 65201