The most commonly used non-invasive method of capturing a snapshot of the gut microbiome is by using a fresh fecal sample; whether from a human or an animal. Fresh fecal samples contain rich microbial communities —  a representation of the microbial community existing in the gut — but proper conditions are required to maintain the integrity of this microbiome until it reaches the lab. 

Microbiome Insights has decades of experience working with Brett Finlay and Bill Mohn’s labs working on models of disease. There are many applications for the use of fecal samples, each one unique and can be facilitated through our expertise.

Our expertise includes:

  • Advanced extraction methods for consideration of particularly robust microbes in the system
  • Inclusion of negative controls to eliminate confounding results
  • rRNA gene sequencing to determine, at a high level, the role of various microbes and the shifts in the microbiome over time depending on implementation
  • Shotgun metagenome sequencing for a higher resolution of both taxonomic and functional outputs
  • Short Chain Fatty Acid Analysis
  • Bioinformatic reporting with a firm understanding of advanced analysis

Services We Offer


DRY SWABS: For dry swabs we recommend using the Becton-Dickinson, BBL CultureSwab EZ II which includes a double-swab encased in a rigid non-breathable transport tube. For all other dry swabs make sure to keep the wrapper for transport to our lab. It is recommended to use two swabs (or one BD DBL CultureSwab II) to maximize your DNA content per sampling session. Samples should be stored in the -80 (preferably not the -20) and shipped to our lab on dry ice; overnight or two day shipping.

WHOLE STOOL: Fecal samples may be collected whole, using any container that can withstand the -80.

  • For human samples, be sure to provide the donor with a toilet bowl collector to ensure the sample does not touch the toilet water. The minimum sample amount we can work with is 50mg. 
  • For animal samples such as companion animals, try to avoid other materials contaminating the sample.
  • For rodent samples it is best to collect 3-5 pellets per rodent to ensure a high volume of sample to work with.

Samples should be stored in the -80 and shipped to our lab on dry ice; overnight or two day shipping.

DEVICES WITH BUFFER: Both Norgen Biotek and DNA Genotek Inc. are manufacturers of biological specimen collection devices that incorporate a lytic stabilization buffer for storage at ambient temperature. See the Resources section below for a quick link to the recommended kits (for collection from human and animal donors). Please refer to each manufacturer for more details on shelf life and stability. Samples collected in these devices can be stored at room temperature and need not be shipped on dry ice.