With the MycoTOX Test we can identify mycotoxin (mould and toxins) exposures and make recommendations for detoxification treatments that have been shown to be effective.
The Microbiome Explorer Comprehensive Stool Test (Formerly MetaXplore™ GI Plus) is one of the most advanced gut microbiome stool tests available in the UK. Developed by Microba, it uses whole-genome shotgun metagenomic sequencing — a method that reads every piece of DNA in your stool sample to identify not just which microbes are present, it also shows what those microbes are actually doing — which metabolites they produce, which compounds they consume, and how that affects your gut environment.
Alongside the microbiome profile, the test also assesses how well your digestive system is functioning and screens for harmful gut infections — all from a single stool sample collected at home.
It is particularly useful for people with persistent digestive symptoms, chronic fatigue, skin conditions, mood issues, or suspected gut infections who want a thorough, evidence-based picture of their gut health. It is also a strong choice for those who have already done a basic gut bacteria test and want more clinical depth.
The Microbiome Explorer Comprehensive Stool Test analyses three areas from a single stool sample:
Microbiome Profile – The core of the test, Results are grouped into 16 key functional areas. , capable of identifying over 28,000 microbial species using whole-genome shotgun metagenomics, it sequences every piece of microbial DNA in your sample — checking for bacteria, archaea, fungi, and parasites. A typical healthy gut contains between 110 and 244 but individual diversity can hugely vary making this new shotgun sequencing so valuable.
A 2024 study confirmed this method provides significantly better resolution than standard gut sequencing approaches (Sanguineti et al., 2024, mSystems.: https://pubmed.ncbi.nlm.nih.gov/38980053/).
Gastrointestinal Health Markers — 7 markers Seven markers that assess gut function and environment — including inflammation, gut barrier integrity, immune activity, and digestive capacity.
Pathogen Screening — 18 markers Targeted detection of pathogenic bacteria and parasites using RT-PCR — the same technology used in COVID testing — identifying infections that standard NHS stool culture routinely misses.
For a full breakdown of every marker tested, see the FAQ below.
The Microbiome Explorer Comprehensive Stool Test suits people who want a thorough, evidence-based analysis — not a basic overview. It is the right choice if you have ongoing symptoms that have not been explained by standard investigation, or if you have already tried a basic gut bacteria test and want more clinical depth.
You are likely a good candidate if you experience any of the following:
This is an at-home stool test. No clinic visit, no GP referral, no waiting list. Your kit arrives by post, you collect a single stool sample at home, and return it using the prepaid envelope included in the kit.
Your kit includes full written instructions. Please read these before collecting. The following is a summary of what to be aware of beforehand.
Wait 4 weeks before collecting if you have recently had a colonoscopy or barium enema.
Wait 14 days after your last dose before collecting if you are taking:
Wait 3 days before collecting if you are taking:
Do not stop any prescription medication without your doctors consent
Do not collect a sample while menstruating or actively bleeding from haemorrhoids.
If you have difficulty producing a sample, magnesium citrate or a psyllium fibre-based laxative may be used 24 hours before your planned collection time. Distilled water enemas are permitted. Do not use suppositories or mineral oil.
At Smart Nutrition we pride ourselves in offering the best price possible for this test.
As a practitioner with 25 years of experience, I have been genuinely impressed by how much clarity this test provides compared to anything that was available even a few years ago. (Emma Wells IFMCP, Dip ION, mBANT, CNHC)
Most gut tests check for microbes they have been specifically designed to detect — so they can only find what they are already looking for. Whole-genome shotgun metagenomics works differently. It sequences all the DNA in your sample without a predefined target list, which means it can identify any microbial species present — including ones that would never show up on a standard test simply because nobody thought to look for them. On top of that, the Microbiome Explorer Comprehensive Stool Test screens for 18 specific gut infections and includes seven markers that assess how your gut is functioning — including inflammation and gut barrier integrity.
For anyone who wants real answers rather than a basic species list, this is the most comprehensive gut stool test we offer.
Most gut tests sold in the UK fall into one of two categories. Some scan the bacterial community broadly but can only identify microbes to a general category level — think family rather than individual species and strains of species. Others test accurately but only for a fixed list of specific organisms, they can only find what they are looking for — anything outside that list goes undetected.
The Microbiome Explorer Comprehensive Stool Test uses shotgun metagenomics, which works differently. It reads all the microbial DNA in your sample from scratch, with no predefined list, so it can identify every species present — bacteria, fungi, parasites, and archaea — including ones that other tests would simply miss.
A 2024 study confirmed that shotgun metagenomics provides significantly superior resolution compared to standard sequencing approaches. (Sanguineti et al., 2024, mSystems, PMID: 38980053).
The Microbiome Explorer Comprehensive Stool Test is designed to give you a far more complete and clinically useful picture of your gut health than standard testing.
It combines three well-established laboratory methods: whole-genome shotgun metagenomics for detailed microbiome analysis, RT-PCR for accurate pathogen detection, and ELISA for key gut health markers. Together, these provide a depth and reliability of insight that goes far beyond basic stool testing.
Processed in an ISO 15189 Accredited Laboratory
Your test is performed by a laboratory accredited to ISO 15189 by the National Association of Testing Authorities (NATA). This is the gold standard for medical laboratories, confirming high levels of technical accuracy, strict quality control, and consistent, reliable results.
https://nata.com.au
End-to-End Clinical Accuracy
Unlike many microbiome tests, this laboratory’s accreditation covers the entire process — from sample handling through to advanced bioinformatic analysis. That means every stage of your test is held to clinical-grade standards, not just part of it.
Nothing Missed: Comprehensive Microbiome Mapping
The sequencing is benchmarked against the Gut Microbiome Reference Catalogue (GMRC), one of the most extensive databases of gut microbes available. This allows for highly detailed identification of microbial species, helping ensure a more complete and accurate picture of your gut ecosystem.
Clinically Recognised Testing Methods
Key components of the test are CE marked, meaning they meet European requirements for safety, performance, and clinical use.
https://ec.europa.eu/growth/single-market/ce-marking_en
Backed by Published Science
The laboratory’s analytical methods have been independently reviewed and published in peer-reviewed journals, including Frontiers in Microbiology:
https://www.frontiersin.org/articles/10.3389/fmicb.2021.643682/full
Research also shows that metagenomic testing is increasingly being used in clinical medicine to provide a more comprehensive understanding of gut health, helping move testing beyond simple screening into a more advanced diagnostic tool:
Wensel et al., 2022, Journal of Clinical Investigation
Microbial diversity is simply the variety of different species living in your gut. A diverse gut microbiome tends to be more resilient — it has more tools at its disposal and is better at recovering when something knocks it off balance. When diversity drops, the gut becomes less adaptable, and research has consistently linked low diversity to conditions including IBS, IBD, anxiety, and depression.
A 2023 analysis of IBS patients found that different IBS subtypes each had their own distinct microbial patterns, with reduced diversity and lower levels of the beneficial bacteria that produce short-chain fatty acids
Chen et al., 2023. https://pubmed.ncbi.nlm.nih.gov/36601316/).
The Microbiome Explorer Comprehensive Stool Test measures both species diversity and richness, comparing your results against Microba’s Healthy Reference Model so you can see where you stand.
It depends which markers are affected. Elevated calprotectin or lactoferrin suggests active intestinal inflammation. Low butyrate-producing microbes may indicate reduced gut barrier support and increased inflammatory risk. Elevated zonulin points to compromised gut permeability. A positive pathogen result means a specific infection has been identified. Y
our results include a written comment from a GMC-registered GP and a Functional Medicine Practitioner, who will flag what is clinically significant and what it may mean for your health. The report does not prescribe a treatment protocol, because the right response depends on your individual circumstances.
Every Smart Nutrition result includes written comments from a GMC-registered GP and a Functional Medicine Practitioner as standard. If you want a more in-depth review we can refer you to a team of experienced functional medicine & nutritional therapists or GP practitioners to work through your results, discuss your symptoms and history, and put together a personalised plan covering nutrition, supplementation, and lifestyle.
Yes. Zonulin is one of the seven gut health markers included in the Microbiome Explorer Comprehensive Stool Test. In plain terms, it is a marker of how well your gut lining is holding together, imagine it like a show lace, holding the cells together. When zonulin is elevated, it suggests the gut barrier has become leakier than it should be — allowing substances to pass through the gut wall that would not normally get through. This is what people mean when they talk about leaky gut. Research has linked raised zonulin levels to gut inflammation, microbial imbalance, and autoimmune conditions including IBD and rheumatoid arthritis (Kolonko et al., 2023, Nutrients. https://pubmed.ncbi.nlm.nih.gov/37242269/)
The Microbiome Explorer Comprehensive Stool Test does not diagnose mental health conditions, but the gut and brain are more closely connected than most people realise. Research has shown that the balance of bacteria in your gut influences mood, anxiety, and mental wellbeing — partly through the compounds gut bacteria produce, and partly through their effect on inflammation. A systematic review found that both depression and anxiety are consistently associated with higher levels of pro-inflammatory bacteria and lower levels of the beneficial bacteria that produce short-chain fatty acids (BMC Psychiatry, 2025. Read the study here: https://link.springer.com/article/10.1186/s12888-025-06871-8). The Microbiome Explorer Comprehensive Stool Test measures exactly these markers. For people who suspect their mood or mental health may have a gut connection, this test often provides the clearest picture of what is going on.
No. SIBO — small intestinal bacterial overgrowth — requires a breath test, because it involves the small intestine and cannot be assessed from a stool sample. The Microbiome Explorer Comprehensive Stool Test analyses the large intestinal microbiome. That said, it can identify dysbiosis patterns, pathogen presence, and low microbial diversity that are commonly found alongside or following SIBO. If SIBO is your primary concern, see our SIBO breath test options.
The connection between gut health and skin is well established in the research. Dysbiosis — an imbalance in the gut microbiome — has been linked to a range of skin conditions including eczema, acne, and psoriasis, with studies showing that gut inflammation and a compromised gut barrier both play a role in how these conditions develop and progress (Ryguła et al., 2024, International Journal of Molecular Sciences. Read the study here: https://pubmed.ncbi.nlm.nih.gov/38396663/). The Microbiome Explorer Comprehensive Stool Test assesses the specific markers relevant to this relationship — including zonulin (gut barrier integrity), calprotectin (inflammation), and butyrate-producing microbes (gut lining support). It will not diagnose a skin condition, but for people whose skin problems have a gut origin, this is often where the investigation starts.
The 16 areas that the microbiome test markers are grouped into are;
These seven markers assess how the gut is functioning and flag potential clinical issues. Calprotectin and lactoferrin indicate active intestinal inflammation — elevated calprotectin in particular is a well-validated red flag for IBD and other inflammatory conditions (Kolonko et al., 2023, Nutrients, PMID: 37242269). Zonulin reflects intestinal permeability; raised levels suggest the gut barrier has become compromised, which has been linked to conditions from IBD to rheumatoid arthritis. Pancreatic elastase is a non-invasive indicator of exocrine pancreatic function. Secretory IgA reflects mucosal immune activity. Faecal occult blood screens for occult GI blood loss. Faecal pH indicates the overall fermentation environment in the colon.
This panel screens for specific harmful bacteria and parasites using RT-PCR technology — the same highly sensitive method used in COVID testing. It works by detecting the genetic material of pathogens directly from your stool sample, which means it can identify infections that standard NHS culture-based stool tests routinely miss.
This is particularly relevant if you have had ongoing digestive symptoms following travel, a bout of food poisoning, or repeated courses of antibiotics, and nothing has shown up on standard testing.
The 18 pathogens screened for are:
Does the Microbiome Explorer comprehensive test check for Histamine producing bacteria?
Yes, The Microbiome Explorer comprehensive Test checks for histamine producing bacteira.
Does the Microbiome Explorer comprehensive test check for Hydrogen Sulphide producing bacteria?
Yes, The Microbiome Explorer comprehensive Test checks for Hydrogen sulphide producing bacteria.
The Microba Microbiome Explorer can be used for patients under 18, though there are a few practical considerations to be aware of. The healthy reference cohort used to generate results was aged 18–75, which means the Expert Summary that the lab provide to us will not be generated for under-18s. Clinical interpretation will also require cross-referencing age-appropriate reference ranges when reviewing the GI Health Markers so we recomend working wiht a practitioner to help with interpretation of the results.
The test is widely used in paediatric clinical practice. Its rigorous science and validated framework make it a well-regarded choice among practitioners working with younger patients, and some of the largest clinics using Microba are paediatric clinics.
If you would like guidance on interpreting results for a child, please get in touch and we can discuss further.
Collect the single stool sample for the Microba explorer comprehensive stool test on a Monday or Tuesday if you can — this gives your sample the best chance of reaching the UK hub without sitting over a weekend. Post it before 1pm on the day of collection at your nearest Post Office, using the prepaid return envelope in your kit.
This sample report includes the bile acids and SCFA’s add on
All sample reports are for representational and educational purposes only. Biomarkers, references ranges, results, and all other data may differ from actual reports. All data included in no way represents an actual patient. Any comparisons of results to actual patients is completely incidental.
Updated
£399.00
With the MycoTOX Test we can identify mycotoxin (mould and toxins) exposures and make recommendations for detoxification treatments that have been shown to be effective.
£289.00
The UK’s most comprehensive genetic methylation test using the Gary Brecka method. Simple home cheek swab kit — includes GP and Functional Medicine Practitioner comments with your results
The Advanced Intestinal Barrier Assessment is a useful test to consider if you suspect you have intestinal permeability or “leaky gut” and want to know what imbalances may be driving that process.
£625.00
The NutrEval test is the most comprehensive health MOT available. It identifies nutritional deficiencies and insufficiencies for over 125 markers and provides personalised recommendations for each.
Please do not return samples to the laboratories that may arrive after Wednesday 27th March and up to and including Monday 2nd April.
The laboratories are closed from the 28th March – 2nd April for the Easter Holiday.