Shotgun Metagenomics (Base Test): Superior for evaluating overall gut health, species diversity, beneficial microbes, and functional pathways. It measures relative abundance across the entire microbiome rather than hunting for specific isolated pathogens.
Targeted qPCR / Stool Antigen Add-ons: Specifically designed to detect low-abundance or easily degraded organisms (e.g., H. pylori, specific Candida species, or specific parasites) by amplifying targeted genetic regions or isolating stable antigens regardless of overall relative abundance.
Clinical Recommendation: For diagnostic confirmation or screening of specific low-level pathogens, targeted antigen assays or qPCR add-ons should be used alongside whole-microbiome shotgun sequencing.
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