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Tests and diagnostics

Gut microbiome testing, without the marketing.

A stool sample sequenced to profile the bacteria, fungi and (sometimes) short-chain fatty acids in your gut. The science is real. The clinical actionability for most healthy adults is limited, and the marketing is often ahead of the evidence. This is the honest version.

A laboratory workstation running microbial DNA sequencing

How the test works

Three different technologies, three price points.

The technology used matters more than the brand. Shotgun sequencing gives species-level detail; 16S is genus-level; qPCR panels test for named organisms.

  • 16S rRNA sequencing

    The basic entry-level method. Identifies bacterial families and genera but not species or function. Good for broad diversity snapshots. £120 to £280.

  • Shotgun metagenomic sequencing

    Sequences all microbial DNA. Species-level detail, strain identification, functional pathways. What ZOE and Viome use. £280 to £550.

  • qPCR targeted panels

    Amplifies specific organisms. Fast, quantitative, focused on known pathogens (C difficile, Klebsiella, Candida). Used by GI-MAP and Genova GI Effects. £480 to £850, usually via a functional medicine practitioner.

What the report shows

Interesting data. Interpretation is the hard part.

Every provider dresses the numbers differently. The underlying measurements are broadly consistent.

  • Alpha diversity

    How many different species live in your gut. Higher generally correlates with better metabolic health, but individual reference ranges are not clinically validated.

  • Key beneficial bacteria

    Akkermansia muciniphila (metabolic health), Faecalibacterium prausnitzii (anti-inflammatory), Bifidobacterium, Roseburia, and the Prevotella to Bacteroides ratio (linked to dietary pattern).

  • Pathogens

    Clostridioides difficile, Klebsiella, pathogenic E coli strains. Clinically actionable if present at meaningful levels alongside symptoms.

  • Fungi and parasites

    Candida overgrowth, Blastocystis, Giardia. Interpretation is contested for most fungi in asymptomatic people.

  • Short-chain fatty acids

    Butyrate, propionate, acetate. Some reports estimate production from bacterial profiles rather than measuring directly.

  • Personalised food scores

    ZOE and Viome give per-food ratings based on your microbiome plus (for ZOE) blood lipid and glucose response. Evidence for accuracy is modest and mostly company-generated.

UK pricing

What the main UK providers charge.

Prices as of 2026. Practitioner-mediated tests include the practitioner appointment.

Provider Price
Atlas Biomed (16S rRNA) £149
Biomesight (16S rRNA) £120 to £180
ZOE (shotgun) plus PREDICT £299 plus subscription
Viome Full Body Intelligence £350 to £550
Chuckling Goat (16S) £180 to £250
Hurdle Health at-home £180 to £320
Doctor's Data GI-MAP (qPCR) £480 to £650
Genova GI Effects (Nordic Labs UK) £550 to £850

Where testing helps

Situations with a reasonable evidence base.

  • Refractory IBS with suspected SIBO

    When symptoms persist despite standard first-line care. A hydrogen breath test is often more useful for SIBO specifically, but microbiome mapping can help direct next steps.

  • Post-antibiotic diarrhoea

    Especially if prolonged, or if C difficile is a concern. GI-MAP style qPCR is appropriate here.

  • Suspected recurrent C difficile

    Where FMT (faecal microbiota transplant) is being considered. NHS pathway is preferred; private testing supports the conversation.

  • IBD adjunct in research settings

    Not diagnostic, but increasingly used alongside standard IBD care to track treatment response.

Where evidence stops

Marketing that runs ahead of the science.

  • "Gut healing" protocols marketed to asymptomatic people

  • Weight loss claims beyond what evidence supports

  • "Anti-ageing via microbiome" is currently unproven

  • One-off snapshots read as diagnoses when day-to-day variation is huge

  • Reference ranges presented as validated when they are company-derived

The single-sample problem is real. Diet on the days before the test, recent antibiotics, hydration, and normal daily variation all shift the numbers.

The actionable part

What works, regardless of testing.

Evidence-based dietary and lifestyle advice that improves microbial diversity for almost everyone. This is what most personalised reports end up recommending anyway.

  • 30 or more different plant foods per week (the Tim Spector benchmark)

  • 30 g of fibre daily from whole foods

  • Fermented foods most days (kefir, live yogurt, kimchi, sauerkraut)

  • Prebiotics: onions, garlic, leeks, oats, slightly-underripe bananas

  • Limit ultra-processed foods and emulsifiers

  • Moderate alcohol (or none)

  • Regular resistance exercise: has independent effects on the gut

Related pages

Frequently asked

Straight answers before you buy a kit.

  • Are gut microbiome tests accurate?

    Shotgun metagenomic sequencing is technically accurate at identifying which bacteria are present. What is not validated is what those results mean clinically for you as an individual. A single stool sample captures one day, and inter-person variation is huge. Two tests from the same person a week apart can look quite different.

  • Are the results actually actionable?

    For most people without gastrointestinal disease, only at the margins. The core dietary advice that follows any microbiome report (more plants, more fibre, more fermented foods, less ultra-processed) is the same advice that would be given without testing. The test can make the advice feel more personal, which for some people improves adherence.

  • Does UK private medical insurance cover microbiome testing?

    Almost never. It is classed as wellness testing rather than diagnostics. Insurers may cover a stool test that is medically indicated (suspected C difficile, IBD workup) but not the consumer microbiome kits.

  • ZOE versus a traditional microbiome test: what is the difference?

    ZOE bundles microbiome sequencing with two weeks of continuous glucose monitoring, a blood lipid response test, and a coaching subscription. Traditional tests give you a report and leave interpretation to you or a practitioner. ZOE is a programme; a stool test is a data point.

  • Should I get one if I have IBS?

    It depends. If you have not yet tried a properly-supervised low-FODMAP trial, that is the higher-yield first step. If you have refractory symptoms, a hydrogen breath test for SIBO and a targeted stool test via a gastroenterologist tend to be more useful than a consumer kit.

  • Can a microbiome test diagnose disease?

    No. Not IBS, not IBD, not coeliac disease, not colorectal cancer. It can flag pathogens (C difficile, certain parasites) and it can give a general dysbiosis picture, but it is not a diagnostic tool. Any concerning symptom (bleeding, unexplained weight loss, change in bowel habit over 50) needs a gastroenterology assessment, not a home test.

Not sure a kit is the right next step?

Talk to a clinician before you spend the money.

A ten-minute call to work out whether a microbiome test, a SIBO breath test, a gastroenterology referral, or simply better dietary advice is the right first move for you.