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 use this form to request sample collection materials: 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

Contact Information

Requestor Name*


2 mL Tubes

  • Eppendorf Snap Top Tube
  • Category: Multiple

15 mL Tubes

  • Falcon Screw Top Tube
  • Category: Multiple

50 mL Tubes

  • Conical Screw Top Tube
  • Category: Multiple

Environmental Filter

IDEXX BioAnalytics REPLACE Matrix

  • All matrices must be submitted in 50mL Conical tubes. Please order separately, as needed.
  • Category: PCR


Standard Flocked Swab

  • Standard Tipped Flocked Swab
  • Ideal for Fur/Body or Cage swabbing
  • Category: PCR

Mini Flocked Swab

  • Mini Tipped Flocked Swab
  • Ideal for Oral or Nasal swabbing
  • Category: PCR

Skin Brush

  • To be used for species with a thick coat
  • Submit in 50mL Conical Tube. Please order separately, as needed
  • Category: Parasitology

Culture Swab

  • Gel Based Amies or Stuart Media Swabs
  • Category: Microbiology

BD ESwab

  • Flocked swab with liquid Amies media transport tube
  • Category: PCR, Microbiology

Opti-Fecal Swab

  • Non-human Primate Fecal Collection Swab
  • Swab with 2mL Liquid Cary-Blair Media
  • Category: PCR, Microbiology


SAF Vial

  • 30mL vial with scoop filled with sodium acetate-acetic acid-formalin (SAF)
  • Category: Parasitology

C&S Vial

  • 30mL vial with scoop filled with Cary-Blair Media
  • Category: PCR, Microbiology

Water Bottle

  • 120mL with screw top bottle with 50mg sodium thiosulfate
  • Category: Microbiology

Opti-Spot Collection

Opti-Spot Cards

  • Specialized absorbent material for collecting dry blood spots
  • 5 Strips/Card
  • Ship with Silica Packs. Please order separately, as needed.
  • Category: Serology


  • 2g packets used for absorbing moisture
  • Category: Serology

Specimen Bags

Specimen Bags

  • Standard 6x9 with pouch
  • Category: Multiple

Animal Health Monitoring Online Submission Guide

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



To submit samples, please login to your account.

If you do not have an account, please fill out the new client registration form below, and our CSS team will assist in getting your account created.