Foundations
Core concepts behind microbiome reports, what each idea explains, where the evidence is strong, and where commercial panels tend to overreach.
Start here
If you have a report in hand, begin with the hub, then use the grouped articles below for mechanism depth. 8 articles are listed here; 31 more are in development (direct links work but show a work-in-progress notice).
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Reading your microbiome report
Consumer gut microbiome reports list taxa, diversity scores, and proprietary indexes at one timepoint. This hub maps common report elements to what they can and cannot indicate, and which Foundations pages explain the underlying biology.
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Multi-marker report synthesis
Consumer reports combine taxa, diversity scores, pathway flags, and proprietary indexes that often conflict. This page explains how to weight markers, resolve common contradictions, and prioritize symptoms and clinical tests over a single health score.
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Dysbiosis
Dysbiosis means altered microbial community structure relative to a reference , in research, diet, antibiotics, or disease cohorts. Consumer reports compress this into proprietary balance scores with no universal healthy template and no standardized clinical cut-offs.
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Red flags, when to seek clinical care first
Certain gut symptoms, unintentional weight loss, rectal bleeding, nocturnal diarrhoea, anaemia, or new symptoms after age 50, require medical evaluation before microbiome tests or restrictive diet experiments. A normal consumer panel does not rule out organic disease.
Using your report
What common scores and labels mean, how to compare results over time, and where sequencing falls short.
Diet & fermentation
Fiber, FODMAPs, SCFAs, and supplements, the mechanisms behind most diet advice on consumer panels.
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What are FODMAPs?
FODMAPs are short-chain carbohydrates that are poorly absorbed in the small intestine and fermented in the colon, where they can trigger bloating, pain, and altered bowel habits in sensitive people.
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Short-chain fatty acids (SCFAs)
Short-chain fatty acids, mainly acetate, propionate, and butyrate, are fermentation products of gut bacteria. They link diet, microbiome composition, and host metabolism, but consumer tests usually infer SCFA capacity from taxa rather than measuring SCFA directly.
Barrier & inflammation
Intestinal permeability, inflammatory markers, and metabolic endotoxemia, separate threads often merged on reports.