Why It's Impossible to Treat Chronic Gut Dysfunction at the Bacterial Level — Layer 1: The Microbiome Tests Are Reading the Mirror, Not the Cause

Start with what everyone else starts with &#8212; the stool test. Here&#8217;s what I keep finding: What the stool test actually measures A stool test like GI-MAP or a Vibrant Gut Zoomer looks at two things. First, it counts bacteria &#8212; which species are present, in what amounts, and whether they&#8217;re above or below the reference range that the lab has built up from healthy controls. Second, it measures the products bacteria make &#8212; short-chain fatty acids, bile acid metabolites, compounds like ammonia and phenol and TMAO, digestive markers like fecal fat and pancreatic elastase, immune markers like calprotectin and sIgA. In theory, this gives you a snapshot of the ecosystem and how it&#8217;s functioning. In practice, here&#8217;s what I keep seeing in patients with chronic gut dysfunction: Butyrate production capacity &#8212; intact. Shotgun sequencing data across cases shows butyrate-producing gene capacity in the 800&#8211;1,200 rpkm range in patients whose guts are severely dysfunctional. What this means in plain terms: the microbial machinery to produce butyrate is fully present. The organisms are there. The genes are there. The butyrate is being made. Stool SCFA panels confirm butyrate output in the adequate-to-high range even in symptomatic clients. So butyrate is not the supply problem &#8212; which is what everyone assumes. Facultative anaerobe expansion