What the gut microbiome actually does
The microbiome is not a passive passenger. It produces vitamins (notably B12, B2 and vitamin K), ferments dietary fibre into short-chain fatty acids that feed the colon lining, trains the immune system and influences the gut-brain axis — the bidirectional signalling pathway between the gut and the central nervous system.
This axis explains why gut disruption is associated with mood disorders. Roughly 95% of the body's serotonin is produced in the gut. Microbiome composition affects the production of neurotransmitter precursors in ways that are still being mapped.
Signs of poor gut health
- Frequent bloating, gas or abdominal discomfort
- Irregular bowel habits — alternating constipation and loose stools
- Food intolerances that weren't previously present
- Frequent infections — suggesting impaired immune training
- Unexplained fatigue
- Skin conditions including eczema, acne and rosacea
- Mood symptoms — anxiety, low mood, brain fog
Clinical tests for gut health
If your GP suspects a gut condition, they may order: stool tests for blood (faecal occult blood or faecal immunochemical test — FIT), stool cultures to identify bacterial or parasitic infections, stool tests for calprotectin (a marker of gut inflammation, useful in distinguishing IBD from IBS), and breath tests for hydrogen or methane to detect small intestinal bacterial overgrowth (SIBO) or lactose intolerance.
Microbiome sequencing tests are available commercially but are not currently used in standard clinical practice for diagnosis. The science is advancing rapidly but the evidence base for interpreting individual microbiome reports is not yet mature enough to guide clinical decisions.
What genuinely improves gut health
The evidence for dietary interventions is more robust than for any supplement. A high-fibre diet — particularly one that includes a variety of plant foods — is the single most impactful change for microbiome diversity. The American Gut Project found that eating 30 or more different plant species per week was associated with dramatically greater microbiome diversity than eating fewer than 10.
- Increase dietary fibre — vegetables, legumes, whole grains, fruits, nuts and seeds all count
- Include fermented foods — yoghurt, kefir, kimchi, sauerkraut and tempeh contain live cultures
- Limit ultra-processed foods — associated with reduced microbiome diversity in multiple studies
- Avoid unnecessary antibiotics — they disrupt the microbiome and the disruption can persist for months
- Exercise regularly — even moderate physical activity correlates with greater microbiome diversity
When to see a doctor
Persistent changes in bowel habits, blood in the stool, unexplained weight loss, or pain that wakes you from sleep are red-flag symptoms that require clinical investigation. Do not self-manage these with dietary changes alone.