Why is H. pylori difficult to detect via standard shotgun metagenomic stool testing?

Helicobacter pylori colonizes the gastric mucosa of the stomach rather than the lower colon. Because of its location:

1. Only tiny amounts of H. pylori cellular material are shed into the digestive tract.

2. Gastric acid, enzymes, and the long transit time through the small and large intestines heavily degrade the bacterial DNA.

3. By the time it reaches stool, intact H. pylori DNA is often well below the 0.005% relative abundance sequencing cutoff.

If H. pylori is suspected clinically, we recommend using a dedicated Stool Antigen Test (available as an add-on to PRO kits) or a clinical urea breath test/biopsy.