Real-time PCR counts the number of a specific bacterial type or species found in a mixed sample

To find out the post-digestion survival rate or see the impact on the intestinal microbiota, we use a standardized procedure that allows us to characterize each type of microorganism in the samples collected. The major advantage of using real-time PCR is its ability to clearly distinguish the different groups of bacteria. For a real quantification, the PCR reaction is coupled with propidium monoazide (PMA) which eliminates dead and damaged cells so that only viable cells are counted while including stressed cells. This technology is beneficial when bacteria are located in a hostile environment such as the stomach or duodenum, or in a competitive environment such as the large intestine.


Method developed for the 7 major groups found in the intestinal microbiota:

  • Bacteroidetes
  • Clostridium leptum group
  • Blautia coccoides group
  • Bifidobacterium ssp.
  • Lactobacillus ssp.
  • Enterobacteriaceae

Advantages of real-time PCR with PMA

  • Specific to genre or species
  • Does not take dead or damaged cells into account
  • Count includes cells that are stressed but still viable

Even more benefits of using real-time PCR

Possibility of developing customized experiments while distinguishing between species from the same genre (ex: Lactobacillus acidophilus vs Lactobacillus casei vs Lactobacillus delbruecki).