Are microbiome tests worth it?

Depends on what you want. For curiosity and trend-tracking after a deliberate intervention, yes. For diagnosing or treating a specific condition, mostly no, you'd be better off seeing a gastroenterologist with the £150-£300 you'd spend. ZOE's strength is the broader programme around the test, not the test alone.

How often should I retest?

If you're tracking an intervention (new diet, antibiotic recovery, supplement), 3-6 months apart makes sense. Monthly is too noisy. Annually is reasonable for general curiosity.

Can the test tell me if I have SIBO?

No. Stool tests sample colonic bacteria. SIBO is small intestinal overgrowth and requires a hydrogen breath test or small bowel aspirate to diagnose. A stool test can be normal in someone with SIBO.

Is the same brand reliable across two samples?

Reasonably. Within-brand reproducibility is generally 70-90% for the major species. Across brands, results vary much more because of different sequencing methods and reference databases. Stick with one brand for trend-tracking.

Microbiome test

Also called gut microbiome test, stool microbiome test.

Dr Chad OkayFounder, Suna Health

3 min read. Updated 10 September 2026.

A microbiome test is a stool sample sequenced to identify the bacteria in your gut. Consumer brands include ZOE, Viome, BiomeSight and Tiny Health. Useful for tracking changes over months and ruling out major dysbiosis. Less useful for specific dietary guidance: the science of 'eat X to fix Y' is still early, and many recommendations are pattern-matched rather than mechanistically validated.

How they work

Disclosure: this entry is published by Suna Health, which is building a consumer gut-health product (a wearable, not a stool test). The companies discussed here compete for the same gut-health spend. We have kept the comparison to what the published evidence supports, but read it knowing who wrote it.

You collect a stool sample (usually a small swab from toilet paper) and post it. The lab extracts DNA, sequences either the 16S rRNA gene (cheaper, identifies bacteria to genus level) or shotgun metagenomics (more expensive, identifies to species/strain and includes fungi and viruses). An algorithm compares your bacterial profile to a reference database and produces a report.

What they're good at

Tracking changes over months: did your fibre intervention shift Bifidobacterium up?
Spotting major dysbiosis (very low diversity, missing keystone species like Akkermansia or Faecalibacterium).
Identifying overgrowth of pro-inflammatory species in some inflammatory bowel disease (IBD) or post-antibiotic states.
Educational: many people understand their gut better after seeing the data.

What they're not good at

Diagnosing disease. They are not regulated medical tests.
Telling you exactly what to eat. The 'eat broccoli for your low Faecalibacterium' style of advice is mostly pattern-matched, not personalised in the way marketing implies.
Capturing function, only composition (16S tests). Two people with the same bacteria can produce very different short-chain fatty acid profiles.
Day-to-day stability. Your microbiome shifts substantially with diet within days, so a single snapshot is limited.

Comparing the major brands

ZOE: combines microbiome with blood lipid response and CGM data; the largest published research programme (PREDICT) behind a consumer test, focused on personalised nutrition. UK and US.
Viome: shotgun metagenomics + RNA sequencing (claims to measure activity not just composition). Strong marketing claims; mixed independent validation.
BiomeSight: 16S, cheaper, more research-friendly. Good if you want to track over time without a subscription.
Tiny Health: focused on infants and pregnancy. Strongest in early-life microbiome.
Onegevity / Ombre / Thryve: similar 16S consumer tests with food recommendations.

What to do with the results

Look at diversity. Higher Shannon diversity index correlates with better metabolic health across most studies. Aim to maintain or grow it over time.
Check keystone species. Are Akkermansia, Faecalibacterium prausnitzii and Bifidobacterium present in reasonable amounts?
Note any massive overgrowths. A large Proteobacteria expansion has been proposed as a potential signature of dysbiosis and may be worth discussing with a doctor.
Track over 3-6 months, not on the day. A single snapshot is noise.
Don't follow restrictive diet rules from a stool test alone. Most should be reviewed with a registered dietitian if you're considering major changes.

Common questions

Are microbiome tests worth it?: Depends on what you want. For curiosity and trend-tracking after a deliberate intervention, yes. For diagnosing or treating a specific condition, mostly no, you'd be better off seeing a gastroenterologist with the £150-£300 you'd spend. ZOE's strength is the broader programme around the test, not the test alone.
How often should I retest?: If you're tracking an intervention (new diet, antibiotic recovery, supplement), 3-6 months apart makes sense. Monthly is too noisy. Annually is reasonable for general curiosity.
Can the test tell me if I have SIBO?: No. Stool tests sample colonic bacteria. SIBO is small intestinal overgrowth and requires a hydrogen breath test or small bowel aspirate to diagnose. A stool test can be normal in someone with SIBO.
Is the same brand reliable across two samples?: Reasonably. Within-brand reproducibility is generally 70-90% for the major species. Across brands, results vary much more because of different sequencing methods and reference databases. Stick with one brand for trend-tracking.

Sources

Navigating microbiome variability: implications for research, diagnostics, and direct-to-consumer testing (2025) (Frontiers in Microbiology)
Evaluating replicability in microbiome data (within-lab 87% vs across-lab 55% genus-level classification) (Briefings in Bioinformatics)
Is the current regulatory framework for direct-to-consumer microbiome-based tests sufficient to protect consumers (NIST cross-company inconsistency; FDA wellness exemption) (Journal of Law and the Biosciences)
Personalised nutrition by prediction of glycemic responses, Zeevi et al 2015 (Cell (PMID 26590418))
Human postprandial responses to food and potential for precision nutrition (ZOE PREDICT 1), Berry et al 2020 (Nature Medicine (PMID 32528151))
Microbial resolution of whole genome shotgun and 16S amplicon sequencing (genus vs species, viral/eukaryote detection) (PLOS One)
Commercial gut microbiome testing: BDA guidance (testing not advised, diet recommendations not yet supported) (British Dietetic Association)
Akkermansia muciniphila and Faecalibacterium prausnitzii reduced in IBD colonic mucosa, Lopez-Siles et al 2018 (Frontiers in Cellular and Infection Microbiology)
Markers of metabolic health and gut microbiome diversity: NFBC1966 and TwinsUK cohorts (BMC Microbiology)
Diet rapidly and reproducibly alters the human gut microbiome, David et al 2014 (Nature (PMC3957428))
Proteobacteria: microbial signature of dysbiosis in gut microbiota, Shin et al 2015 (Trends in Biotechnology (PMID 26210164))
Hydrogen-Methane Breath Testing to Diagnose SIBO (SIBO is small-intestinal, not colonic) (Clinical and Translational Gastroenterology)