🦠 Gut health & digestion
5 mechanistic pathways · 75 options
Almost every gut complaint traces to one of five things: a damaged barrier, a disordered microbial community, motility running too fast or too slow, insufficient digestive output, or something growing where it shouldn't. They produce overlapping symptoms and need opposite treatments — feeding the microbiome with prebiotic fibre makes SIBO dramatically worse, which is the single most common self-treatment mistake in this area.
The pathways
Barrier integrity & mucosal repair
A single layer of epithelial cells separates you from several pounds of bacteria. Tight junctions, the mucus layer and rapid epithelial turnover maintain that separation; when they fail, bacterial products reach the immune system and drive inflammation well beyond the gut.
Microbiome composition & prebiotic substrate
The colonic microbiome ferments what you cannot digest into short-chain fatty acids that feed the gut lining and regulate immunity system-wide. Diversity is the most consistent marker of a healthy community — and the important caveat is that everything here worsens small-intestinal overgrowth.
Digestive output — acid, enzymes & bile
Bloating an hour after eating, undigested food, and feeling heavy after fat are output problems, not microbiome problems. Stomach acid falls with age and with PPI use; bile flow drives fat digestion and the excretion of everything the liver conjugates.
Motility, IBS & the brain-gut axis
The gut has its own nervous system with more neurons than the spinal cord, and it talks to the brain continuously. IBS is a disorder of that communication as much as of the gut itself — which is why psychological interventions genuinely outperform most drugs in trials.
Overgrowth, dysbiosis & antimicrobials
SIBO, SIFO and H. pylori all involve organisms in the wrong place or in the wrong numbers. This is the pathway where prebiotics make things worse and where the sequence — kill, then clear biofilm, then re-establish motility — determines whether it comes back.
Test before you choose a pathway
Every route below can be argued for on mechanism. Only bloodwork tells you which one is actually your problem — and picking the wrong pathway is the most common reason someone concludes "none of this works". Across all 5 pathways, these are the 12 markers worth having in front of you first.
Ordered together:
🌱 Gut Health & AbsorptionYou have the pathways. Here is the stack.
The Gut Health Blueprint names the one compound I would start with in each of these 5 pathways, what it was chosen over, and why — plus 20 options to swap in or stack on top, every one of them priced and linked.
Open The Gut Health Blueprint →The protocols behind these
Dosing, stacking and cycle timing live inside the Academy, alongside the full interactive Vault and the Bloodwork Protocols.
Join the Academy — $10/mo →← Open Gut health & digestion in the interactive Vault · All 21 goals
Frequently asked questions
This goal is broken into 5 distinct mechanistic pathways — Barrier integrity & mucosal repair; Microbiome composition & prebiotic substrate; Digestive output — acid, enzymes & bile; Motility, IBS & the brain-gut axis and others — across 75 compounds and supplements. Each pathway is a different argument about how the body gets there, so the useful question is which one matches where you are actually stuck.
The one that matches your actual limitation, which bloodwork usually settles faster than guessing. An appetite drug does nothing for someone who already undereats, and a thyroid intervention does nothing if your thyroid is fine. Each pathway page lists the markers that tell you whether it is your problem.
No. The 5 pathways are listed in mechanistic order, not by strength of evidence, and neither are the 75 options inside them. A lot of what works in this space has never had the trial run, and sorting by trial count would bury exactly the compounds you came looking for.