For individuals
Your microbiome is an ecosystem, not a score.
There is no single ideal microbiome. What matters is the relationship between your food, your rhythms, your movement, your exposures, your symptoms and your context. Seven domains, seven evidence-based actions, and an honest signal of how strong the evidence is for each.
The seven domains
Seven places to act, with the evidence for each.
01
Plant diversity
Different plant foods feed different ecological niches. Count distinct plants across a week — vegetables, fruit, pulses, whole grains, nuts, seeds, herbs and spices. Add one new plant rather than redesigning every meal.
Moderate — and the number 30 is a comparison bin from one citizen-science cohort, not a threshold
02
Fibre and resistant starch
Microbes ferment certain fibres into short-chain fatty acids. Responses differ sharply between people and with the starting diet; a rapid increase can make bloating worse. Pick one source, increase slowly.
Mechanism solid — individual response highly variable
03
Fermented foods
A 2021 Stanford trial found a fermented-food diet raised diversity and lowered inflammatory markers. A larger 2025 trial did not replicate it. Live-culture yoghurt or kefir, or refrigerated fermented vegetables, remain a reasonable small addition — but not a settled intervention.
Promising, then partly un-replicated in 2025 — treat as unsettled
04
Polyphenol-rich foods
The colour compounds in berries, cocoa, tea, coffee, herbs and olive oil interact with gut microbes in both directions. Effects depend on dose, food matrix and your own metabolism. Prefer foods to high-dose extracts.
Moderate — heterogeneous foods, heterogeneous effects
05
Rhythm, meals and sleep
Gut microbial activity follows daily rhythms tied to meals and the sleep–wake cycle. Keep a reasonably constant wake time and a repeatable overnight eating pause — without letting time-restricted eating become under-eating.
Emerging — and rhythm supports health well beyond any microbial effect
06
Movement
Exercise can shift some gut microbial traits, but changes depend on body composition and appear to reverse when training stops. Movement keeps its clear health value even where the microbial effect is uncertain.
Moderate for health — preliminary for specific microbial effects
07
Microbiome stewardship
Antibiotics cause a marked, person-specific disruption with incomplete recovery — and remain essential medicines when indicated. Take them exactly as prescribed; never skip a necessary treatment to “protect” your microbes. Persistent digestive symptoms deserve assessment, not self-medication guided by a commercial score.
See a doctor for blood in stool, weight loss, fever, anaemia, night-time symptoms or a persistent change.
Solid for antibiotic disruption — testing usefulness still limited
Photo to addA figure from your microbiota work, or one of the kefir photographs.
Read the evidence
What “evidence-based” means here.
The microbiome is responsive, but not infinitely controllable. These actions were selected because they rest on a plausible mechanism, on human data, and on low practical risk for most adults. The strength of evidence is not the same across domains — which is why it is printed on each one — and a change in microbiota composition is not automatically a health benefit.
One consequence worth stating plainly: a single stool sample does not estimate your own average. For most bacterial genera, your day-to-day variation exceeds the variation between different people. Any test that gives you one number from one sample is reporting noise with a decimal point.
This is a self-reflection guide. It is not a diagnostic test, not a detox, and not a substitute for medical care.
- Joos R, et al. — Examining the healthy human microbiome concept. Nature Reviews Microbiology 23:192–205, 2025.
- Vandeputte D, et al. — Temporal variability in quantitative human gut microbiome profiles. Nature Communications 12:6740, 2021.
- McDonald D, et al. — American Gut: an open platform for citizen science microbiome research. mSystems 3:e00031-18, 2018.
- Wastyk HC, et al. — Gut-microbiota-targeted diets modulate human immune status. Cell 184:4137–4153, 2021.
- Deehan EC, et al. — Precision microbiome modulation with discrete dietary fiber structures. Cell Host & Microbe 27:389–404, 2020.
- Dethlefsen L & Relman DA — Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. PNAS 108:4554–4561, 2011.
Next step
Start with one honest conversation.
Twenty-five minutes. Bring the thing that actually bothers you, not a tidy version of it.