Why might a pathogen (like H. pylori) test positive on a standard clinical antigen/qPCR test but show 0% on a Tiny Health Shotgun Metagenomics report?

This difference stems from the fundamental distinction between targeted clinical assays and comprehensive microbiome profiling:

• Targeted Assays (Antigen / qPCR): Focus on a single organism and detect specific proteins (antigens) or amplified target DNA sequences. Protein antigens and short DNA fragments often remain stable and detectable even after degrading through the GI tract.

• Shotgun Metagenomics: Sequences all microbial DNA in a sample to provide a complete picture of the overall gut ecosystem. However, organisms that reside high in the GI tract (such as gastric H. pylori) undergo significant DNA breakdown during transit through the stomach and intestines.

• Relative Abundance Threshold: Tiny Health’s medium-depth shotgun sequencing reports taxa down to a relative abundance threshold of 0.005%. If an organism's intact DNA falls below this cutoff due to degradation or low stool shedding, the report will list it as 0%.

Key Takeaway: A 0% result on a shotgun metagenomic report means "not detected above the 0.005% relative abundance threshold," not necessarily "completely absent."