What are the different types of GI Microbiome Testing?

Generally speaking, there are three main types of gut microbiome tests: microscopy, PCR, and culture.


Microscopy testing is the oldest and simplest type of gut microbiome test. It involves examining a stool sample under a microscope to identify and count the different types of bacteria. However, microscopy is not very sensitive and can only identify a limited number of bacteria, fungi, and parasites. It is also dependent on the aptitude of the laboratory technician performing the assessment which can lead to varying results and has a high probability to miss identify problematic bacteria, fungi, and parasites.  

PCR (polymerase chain reaction)

PCR testing is a highly sensitive and specific type of gut microbiome test. It involves amplifying DNA from a stool sample, which allows for the identification of a wider range of markers within stool samples.

PCR is more quantitative than microscopy, as it also measures the abundance of different markers testing. This allows even . 


Culture testing is a comprehensive type of gut microbiome test. It involves growing bacteria from a stool sample in a laboratory. This allows for the identification of the bacteria that are present in the stool sample. Culture testing is the most time-consuming and expensive type of test.

Most GI Microbiome profiles utilize all 3 of these testing types to provide testing with a wide range of relevant markers. It is important to look for GI testing profiles that utilize PCR testing for the majority of its markers as this will provide test results that are more comprehensive with better accuracy allowing you to create a treatment protocol that is better aligned to patient needs. 





Simple, inexpensive, and quick Not very sensitive or specific
PCR Fast, sensitive, specific, and quantitative Requires expensive technology
Culture Comprehensive Expensive and time-consuming


Three GI Microbiome profiles that focus largely on PCR testing are the 

To learn more about the profiles and the types of Bacteria, fungi, and Parasites tested you can visit https://www.usbiotek.com/gi-microbiome-testing