North America

Microbiome Analysis 

Sample Collection & Shipping Guidelines

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). 
    1. Sample ID (minimum).
    2. Treatment group, if applicable.
    3. 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. 


Fecal Collection and Shipping SOP
for Germ-free Animal Monitoring

Sample Collection & Shipping Guidelines

Germ-free Complete Profile

Feces: Fecal pellets should be collected aseptically and placed in individually labeled sterile tubes.

If testing individual mice/rats, submit fecal pellets from each animal. Two to three pellets per animal is adequate.

If collecting fecal pellets from multiple animals, gloves should be changed and forceps replaced between animals to prevent cross-contamination. Alternatively, forceps can be wiped clean and immersed in diluted bleach (10%) solution for 10 minutes prior to reuse.

Fecal samples should be stored in the refrigerator until ready to send.

Place labeled sample tubes in a styrofoam box and ship overnight to our laboratory. Samples should be shipped on ice packs.


Have questions or need additional information?

Let's get you connected to an experienced account manager or customer support representative. Call 1-800-669-0825 or 1-573-499-5700, email or fill out the form below.

Sample Collection Kit Request

Please click the button below to go to our Animal Health Monitoring request sample collection materials form, where you can request Opti-Spot® cards, swabs, tubes, or REPLACE® matrices. Requested supplies will ship within 4-7 business days via FedEx. In order to help clients manage resources, we suggest ordering supplies to cover 3 months’ worth of testing.
If you have questions regarding order status, tracking, or changes to your order, please contact us at For all other inquiries, please contact
Sample Collection Materials Form

NHP Sample Collection Kit Request

Please click the button below to go to our NHP request sample collection material form. We suggest ordering supplies to cover 3 months’ worth of testing. If you have questions about quantities or would like assistance determining items and quantities, please contact us:
NHP Sample Collection Materials Form

Animal Health Monitoring Online Submission Guide

A quick reference guide to Animal Health Monitoring sample submissions in our online  portal.