Microbiome diagnostics is dazzling technology, but a test only matters when its result actually changes the treatment decision.
16S rRNA sequencing is cheap and well-validated, reliably revealing the major bacterial groups — yet it sees only part of the gut ecosystem.
Shotgun metagenomics reads the sample's entire DNA for a richer picture, but the interpretive uncertainties don't disappear — they merely shift.
Relative ratios can mislead; quantitative profiling and Dynamap measure absolute cell counts — a real advance, though they still don't resolve the question of interpretation.
Metabolomics measures not who is present in the gut but what they produce — capturing function directly, not just microbiome composition.
Every microbiome testing method has its strengths and blind spots; this chapter compares them and shows what each can genuinely do in the clinic.