Your Complete Guide to Microbiome Testing

Three at-home stool tests. One sample, collected at home, results in about two weeks. The difference is how deep a look you want.

Microbiome Check — $239 78 markers · traditional culture + MALDI-TOF (we grow the microbes from your sample and identify them). An affordable first look at the balance of bacteria and yeasts in your gut. Order the Microbiome Check →

Complete Microbiome Mapping (GI-MAP) — $569 134 markers · DNA-based PCR (a gut DNA test that checks a set list of organisms). The comprehensive DNA panel — bacteria, pathogens, parasites, plus digestion, inflammation and gut-barrier markers. Order Complete Microbiome Mapping →

Advanced Microbiome GutIQ — $599 Shotgun metagenomic sequencing · screens 28,000+ microbial species (reads all the DNA in your sample) The deepest view — species-level detail, an interactive Species Explorer, and functional insight. Order the Advanced Microbiome GutIQ →

Not sure which one? Compare all three side by side ↓ · or browse gut health testing

No referral needed · collect at home · NATA-accredited laboratory

Prefer the detail first? The full side-by-side comparison is here, and the three tests are explained in plain language throughout this guide.

Inside your digestive tract lives a community of trillions of microorganisms — bacteria, yeasts, viruses and more. Collectively they're known as your gut microbiome, and they're far more than passengers. This community behaves like an organ in its own right: it helps digest your food, makes certain vitamins, helps train your immune system, keeps the lining of your gut healthy, and even sends signals to your brain.

To put the scale in perspective, your gut is home to an estimated 10 trillion-plus microorganisms carrying millions of genes — many times more genetic material than your own body. That's a vast metabolic workforce doing jobs your own cells simply can't.

When that community is thriving — diverse, well-balanced, and doing its job — your gut tends to look after you quietly in the background. When it's disrupted — less diverse, missing some of its most useful members, or overrun by the wrong organisms — the effects can be felt well beyond the gut.

A microbiome test is a way to see that community: who's living there, whether it's balanced, and what it's producing. This guide walks you through what that means, how the different tests work, and what testing can (and can't) tell you.

Think of it as an ecosystem, like a forest or a reef. A healthy ecosystem isn't defined by a single species — it's defined by diversity (lots of different species), the balance between them, and a few keystone species that hold the whole system together.

Among the jobs your gut microbes do every day:

• Digest what you can't. They ferment the fibres your own body can't break down, releasing nutrients and energy — and producing valuable compounds called short-chain fatty acids (more on these shortly).
• Make vitamins. They synthesise vitamin K and several B vitamins.
• Train and regulate your immune system. A large share of your immune cells sit just beneath the gut lining, in constant dialogue with your microbes.
• Protect the gut lining. Beneficial microbes help maintain the barrier that keeps unwanted substances out of your bloodstream.
• Talk to the rest of your body — including your brain — through nerves, hormones and the compounds they produce.

The key idea running through all of this: it's not just who is there, but what they're doing.

In any ecosystem, a few species do a disproportionate amount of the work. In your gut, several beneficial microbes come up again and again because of how useful they are. A good microbiome test looks specifically at whether these are well represented:

• Bifidobacteria and Lactobacilli — classic "good bugs." They help crowd out less welcome organisms, keep the gut environment slightly acidic, support digestion, and are involved in making vitamins. These are also the families most people recognise from probiotic products.
• Akkermansia muciniphila — a specialist that helps maintain the protective mucus layer lining your gut. Healthy Akkermansia levels are associated with a well-kept gut barrier.
• Faecalibacterium prausnitzii and Roseburia — two of your most important butyrate producers. Butyrate is a compound your gut cells use as fuel, and it's strongly linked to a calm, well-functioning gut (see the next section).

When two or more of these keystone species are running low, the community can look "hollowed out" even if the overall numbers seem fine — which is one reason a good test looks at who is present, not just how many.

One of the most valuable things your microbiome does is turn dietary fibre into short-chain fatty acids (SCFAs). These are a big part of why a healthy gut is good for the rest of you. Three matter most:

• Butyrate — often called the star. It's the main fuel source for the cells lining your colon, helps calm inflammation, and supports a strong gut barrier. Low butyrate is a common finding when the gut is out of balance.
• Acetate — the most abundant SCFA. It travels beyond the gut and is used for energy around the body, and is involved in appetite and metabolism.
• Propionate — involved in how your body handles blood sugar and cholesterol, and in signalling fullness.

The practical takeaway is simple and encouraging: fibre is what feeds this process. The more variety of plant fibres you eat, the more raw material your beneficial microbes have to produce these helpful compounds. This is the mechanism behind a lot of "eat more plants" advice — you're really feeding your butyrate-makers.

Dysbiosis is the word for an imbalance in the gut community that's associated with less-than-ideal health. It's worth knowing that dysbiosis isn't one single thing — it comes in different flavours, and a good test helps tell them apart:

• Lost diversity — fewer different species overall, which tends to make the community less resilient.
• Missing keystones — the helpful specialists (like the butyrate producers) are depleted.
• Overgrowth of opportunists — organisms that are harmless in small numbers become over-represented, sometimes driving inflammation.
• A shift in output — the community may look roughly normal but be producing less of the good stuff (like butyrate) and more of the inflammatory stuff.

Several everyday things can nudge the gut toward imbalance:

• Antibiotics — life-saving when needed, but broad-spectrum courses can deplete beneficial bacteria, sometimes for months. Repeated courses without recovery time have the biggest impact.
• Some medications — including long-term acid-suppressing medicines.
• A low-fibre, low-variety diet — less fuel for your beneficial microbes.
• Chronic stress and poor sleep.
• Chronic constipation and slow transit.
• Gut infections — a bout of food poisoning can shift the community for some time afterward.

Importantly, dysbiosis has been associated with a wide range of conditions — from irritable bowel symptoms and inflammatory bowel disease through to metabolic, immune and mood-related conditions — but associated with is not the same as causes. A test can describe your gut community; it can't, on its own, diagnose any of these conditions.

You may have heard the term "leaky gut." It's often used loosely, but there's real biology underneath it worth understanding.

Your gut lining isn't a single wall — it's a multi-layered defence system:

1. The microbes themselves form the first line, occupying space so unwanted organisms can't take hold.
2. A mucus layer sits on top of the gut wall, kept healthy in part by Akkermansia and by butyrate.
3. A single layer of cells, held together by "tight junctions," forms the physical wall. (These cells renew themselves every few days.)
4. Immune cells sit just beneath, ready to respond — and producing antibodies (secretory IgA) that patrol the gut surface.
5. The bloodstream and lymph beyond, with the liver as the next checkpoint.

"Leaky gut," properly understood, means one or more of these layers isn't working well. That's why a good test looks at several markers that each reflect a different layer:

• Zonulin relates to the "tightness" of the junctions between gut wall cells.
• Calprotectin reflects active inflammation in the gut lining.
• Secretory IgA reflects your gut's front-line immune activity.
• Beneficial flora and mucus-supporting microbes (like Akkermansia) reflect the outer, protective layers.

Rather than a vague label, these give a concrete, measurable picture of how well your gut's defences are holding up. (If gut-barrier health is your main focus, i-screen also offers a dedicated Intestinal Permeability (Leaky Gut) Test.)

Your gut microbiome mostly lives in your large intestine — the biggest and busiest microbial community in your body. A stool sample is the most direct window into it. It captures the DNA of the organisms living there, the ones that are alive and active, the substances they produce, and markers from your own body about how your gut is functioning.

It's also non-invasive — you collect a small sample at home, and it's sent to the lab. No scopes, no fasting, no clinic visit for the collection itself.

Ready to look at yours? The Microbiome Check ($239) covers the essentials; the Complete Microbiome Mapping ($569) adds pathogens, digestion and inflammation markers.

Depending on which test you choose (more on the three options below), an i-screen microbiome test can give you insight into:

How diverse and balanced your gut is. A picture of the overall community — how varied it is, and whether the balance is tilted toward beneficial or less-helpful organisms.

Whether your beneficial "keystone" microbes are well represented — the specialists that support digestion, the gut barrier and a calm gut environment.

What your microbes are producing — in particular, your short-chain fatty acids, including butyrate.

Signs of inflammation, digestion or gut-barrier issues — through the function markers described below.

Whether there are unwanted guests — parasites, yeast overgrowth (such as Candida), and certain disease-causing bacteria, viruses or worms, which sometimes need medical attention.

You don't need to understand every marker. The value is in the overall story: Is my gut community diverse and balanced? Are my helpful microbes doing their job? Is anything out of place?

Beyond the microbes themselves, the more comprehensive tests report several function markers. Here's what they mean in plain language:

• Calprotectin — a marker of inflammation in the gut lining. Raised levels suggest the gut wall is irritated or inflamed.
• Pancreatic elastase — reflects how well your pancreas is producing digestive enzymes. Low levels can point to under-digestion of food.
• Secretory IgA — your gut's front-line immune antibody. Both very low and very high levels tell a story about immune activity at the gut surface.
• Zonulin — relates to gut-barrier "tightness" (the leaky-gut picture above).
• Beta-glucuronidase — an enzyme produced by certain gut bacteria that's involved in how your body processes and recycles substances, including some hormones and toxins.
• Steatocrit — reflects fat in the stool, a clue to how well fats are being digested and absorbed.
• Faecal pH — the acidity of the gut, which shifts with fermentation and the balance of your microbes.

Together, these turn a microbiome test from a simple "who's there" list into a functional read of how your whole digestive system is working.

Which test measures these? Digestion, inflammation and immune markers are included in Complete Microbiome Mapping and Advanced Microbiome GutIQ. Compare all three ↓

One reason interest in the microbiome has exploded is that its influence doesn't stop at the gut. Research increasingly points to two-way "conversations" between the gut and the rest of the body.

The gut–brain axis. Your gut and brain are in constant communication, through several channels: the vagus nerve (a direct nerve line), hormones released in the gut wall, immune signals, and the compounds your microbes make. Butyrate, for example, is being studied for its role in brain health, while inflammatory compounds from an imbalanced gut have been linked to symptoms like fatigue, low mood and "brain fog." It's part of why gut health and mental wellbeing are so often discussed together.

The gut–skin axis. The state of your gut community appears to be linked to skin health and inflammatory skin conditions.

The gut–hormone axis. Your microbiome plays a role in how some hormones — including oestrogen — are processed and recycled in the body, partly through that beta-glucuronidase enzyme mentioned above.

A note on honesty here: this is a fast-moving area of science, and much of it is about associations rather than proven cause-and-effect. A microbiome test won't diagnose a mood, skin or hormone condition. What it can do is give you and your practitioner a clearer picture of your gut, which is one piece of a bigger puzzle.

People come to microbiome testing for all sorts of reasons. Some common ones include ongoing digestive symptoms like bloating, wind, irregular bowel habits or discomfort; low energy; skin concerns; mood changes; or unexplained food sensitivities (which some people explore further with a Food Intolerance (IgG) Test). Others simply want a data-driven baseline as part of looking after their health proactively.

Testing can be a useful starting point in any of these situations — but please read this carefully: a microbiome test is not the right first step for symptoms that need medical evaluation. See your GP promptly if you have any of the following, rather than relying on a test:

• Blood in your stool, or black, tarry stools
• Unexplained weight loss
• A persistent, unexplained change in your bowel habits
• Ongoing or severe diarrhoea, or signs of dehydration
• Fever alongside gut symptoms
• A family history of bowel cancer or inflammatory bowel disease, or you're over the age at which bowel screening is recommended

These need proper assessment. A test complements medical care — it doesn't replace it.

If that sounds like you and none of the red flags above apply, the three at-home tests are compared below — see the comparison ↓

i-screen offers three at-home stool tests for gut health. They differ mainly in the laboratory method used to identify what's in your sample — and the method shapes what the test can tell you. Here's each one in plain language.

1. Microbiome Check — the essential check

How it works: culture and MALDI-TOF mass spectrometry. The lab grows the living microbes from your sample, then identifies them by reading their unique molecular fingerprint. Because it works with living organisms, it's good at confirming what's actually alive and active in your gut.

What you learn: your beneficial bacteria, pathogenic and opportunistic bacteria, yeasts (including Candida), and common parasites — plus digestive clues from the stool's appearance and microscopy (things like undigested food, fat, or hidden blood).

Best for: a solid, affordable first look at the balance of helpful versus unwanted organisms, with some basic digestion insights.

Good to know: this one doesn't measure your microbes' metabolic output (short-chain fatty acids), DNA-level diversity, or inflammation and gut-barrier markers like calprotectin and zonulin.

78 markers · results in ~2 weeks · around $239.

→ View the Microbiome Check

2. Complete Microbiome Mapping (GI-MAP) — the comprehensive DNA panel

How it works: DNA-based PCR. Instead of growing microbes, this detects them by their DNA. It's highly sensitive and specific, can pick up organisms that are difficult to grow (even at low levels), and screens a defined, targeted list of microbes and markers — all from a single stool sample.

What you learn: a much wider picture, built around six groups of organisms — pathogenic bacteria, commensal (normal) bacteria, opportunistic pathogens, fungi and yeasts, viruses, and parasites and worms — plus an overall diversity-and-balance read and H. pylori with its virulence factors and antibiotic-resistance genes. Alongside the organisms sit immune and digestive markers: calprotectin, pancreatic elastase, secretory IgA, zonulin and more, plus your short-chain fatty acids.

Best for: anyone wanting a thorough, sensitive DNA-based picture that combines community balance with digestion, inflammation and barrier markers.

Good to know: this panel looks for a defined, targeted list of organisms. If you want an open-ended read of everything in the sample, that's the Advanced Microbiome GutIQ test below.

134 markers · results in ~2 weeks · around $569.

→ View the Complete Microbiome Mapping (GI-MAP)

3. Advanced Microbiome GutIQ — the most advanced

How it works: shotgun metagenomic sequencing. Rather than looking for a pre-set list, this reads all the genetic material in your sample at once — bacteria, viruses, fungi and other microorganisms together. Because nothing has to be grown in a lab and nothing has to be on a checklist to be found, it can pick up organisms that are difficult or impossible to culture, and it screens against a reference of more than 28,000 microbial species. It's the difference between asking "are these 30 organisms present?" and "what is actually in here?"

What you learn: everything the comprehensive panel covers, plus:

• Species-level identification across the whole community, not just the targeted list — including organisms most panels never look for.
• The richest diversity metrics — Shannon and Simpson indices, and how your community is distributed across phyla.
• A full biochemical picture alongside the organisms: calprotectin and pancreatic elastase, secretory IgA, zonulin, beta-glucuronidase, steatocrit, faecal pH, tissue transglutaminase IgA, and your short-chain fatty acids — butyrate, acetate, propionate and valerate.
• Functional insight — an inferred read of what your microbiome is capable of producing, such as LPS, histamine, TMA and branched-chain amino acids.
• An interactive Species Explorer — rather than a static PDF, your results come with a searchable, colour-coded tool for navigating the organisms found, filtering them, and seeing how your phylum distribution sits.

How it's run: metagenomic next-generation sequencing (mNGS) for the community read, with qPCR, PCR, immunoassay (CLIA, ELISA, FEIA) and GC-MS methods for the biochemical markers — so each analyte is measured by the method best suited to it.

Best for: people who want the deepest, most data-rich view — the fullest picture of not just who is in your gut, but what they're doing.

Results in ~2 weeks · around $599.

→ View the Advanced Microbiome GutIQ

At a glance

Which one is right for you?

• New to gut testing, or want an affordable starting point → Microbiome Check
• Want a thorough, sensitive DNA panel with inflammation, barrier and function markers → Complete Microbiome Mapping (GI-MAP)
• Want the deepest, most complete picture, including what your microbes are producing → Advanced Microbiome GutIQ

Whichever you choose, your results are published to your secure online dashboard — and you can add a dietitian review of your results if you'd like expert help turning them into a plan. Prefer the fullest workup in one go? The Platinum Gut Health Check bundles the Advanced Microbiome GutIQ test with food intolerance, leaky gut and SIBO testing for a complete picture.

We think being clear about the limits is part of doing this well.

• It's not a diagnosis. A microbiome test is an insight tool, not a substitute for medical assessment. It doesn't diagnose, treat, cure or prevent disease.
• It doesn't replace seeing a doctor — especially for the red-flag symptoms listed above.
• Some findings need follow-up. The test can detect certain disease-causing organisms. If one shows up, it may require medical care — and some are "notifiable," meaning the laboratory is legally required to inform public health authorities, and you may be contacted for follow-up. That's the system working as it should.
• Results are best interpreted in context. A number on a report only means so much on its own. Your results are most useful alongside your symptoms, history and goals — ideally with a knowledgeable practitioner.

1. Order your test online and receive your collection kit in the post.
2. Collect your sample at home — a simple stool collection, following the step-by-step instructions in your kit.
3. Send it to the lab in the prepaid packaging. Your sample is analysed in a NATA-accredited laboratory.
4. Receive your results — typically within about two weeks — in your secure online dashboard, and review them on their own or with a practitioner.

A little preparation makes your results more reliable. Your kit will include specific instructions, but in general:

• Antibiotics — these can significantly disturb your microbiome. It's usually best to wait a period after finishing a course before testing, so your results reflect your everyday gut rather than the immediate aftermath.
• Probiotics and some supplements — you may be advised to pause these before collecting, so they don't skew the picture.
• Recent tummy bugs — if you've had a bout of gastro, it's worth letting things settle first (unless you're specifically testing to investigate it).
• Timing — collect a sample that reflects a fairly typical day for you, and follow the kit's instructions on filling the tube to the line, avoiding contamination, and posting promptly.

If in doubt about medications or timing, check with your practitioner or GP before pausing anything.

When your report arrives, a few questions will help you focus on what matters:

• Is my community diverse? Greater diversity generally signals a more resilient gut.
• Are my keystone species present? Healthy levels of the beneficial specialists — especially the butyrate producers — are a good sign.
• What am I producing? Adequate short-chain fatty acids, particularly butyrate, reflect a gut that's being well fed with fibre.
• Is anything out of place? Overgrowths, low beneficial levels, raised inflammation markers, or any pathogens are the things to look at more closely — and to discuss with a practitioner or GP where relevant.

Retesting a few months down the track can show whether the changes you've made are moving things in the right direction — often the most motivating part.

Whatever your results show, the most reliable ways to support a healthy gut community are reassuringly down-to-earth — and a good practitioner can help you personalise them:

• Eat a wide variety of plants. Diversity on your plate supports diversity in your gut. A common goal is aiming for many different plant foods across a week — vegetables, fruits, legumes, whole grains, nuts and seeds.
• Feed your butyrate-makers with fibre. Different fibres feed different microbes, so variety matters as much as quantity.
• Include fermented foods like yoghurt, kefir, sauerkraut and kimchi, which can add beneficial microbes and diversity.
• Enjoy polyphenol-rich foods — colourful fruits and vegetables, extra-virgin olive oil, green tea, herbs and spices — which your gut microbes love.
• Look after sleep and stress. The gut–brain link runs both ways; chronic stress and poor sleep can affect your microbiome.
• Move regularly. Physical activity is associated with a more diverse gut community.
• Use antibiotics wisely. Take them when genuinely needed, and support recovery afterward.
• Go gently. Sudden, drastic diet overhauls can backfire; steady, sustainable changes tend to serve your gut better.

Children's and infants' gut microbiomes are genuinely different from adults' — they're still developing, and what's "normal" changes with age. Results for children should always be interpreted using age-appropriate expectations and, ideally, with a practitioner experienced in this area. A finding that would be unusual in an adult may be perfectly normal for a developing child.

• Microbiome — the whole community of microbes living in your gut (and their genes).
• Dysbiosis — an imbalance in that community associated with less-than-ideal health.
• Diversity — how many different species are present; more is generally better.
• Keystone species — beneficial microbes that do a disproportionate amount of good (e.g. Akkermansia, Faecalibacterium prausnitzii, Bifidobacteria).
• Short-chain fatty acids (SCFAs) — helpful compounds your microbes make from fibre; butyrate is the standout.
• Prebiotic — food (mainly fibre) that feeds your beneficial microbes.
• Probiotic — live beneficial microbes, taken in food or supplements.
• Calprotectin — a marker of gut inflammation.
• Zonulin — a marker relating to gut-barrier "tightness."
• Leaky gut — everyday term for a gut barrier that isn't working well at one or more of its layers.
• Culture + MALDI-TOF — a lab method that grows microbes and identifies them by their molecular fingerprint.
• PCR — a DNA-based lab method that detects microbes by their genetic material; sensitive and targeted.
• Metagenomic shotgun sequencing — a method that reads all the DNA in a sample for the most complete, species-level picture.

Do I need to have symptoms to test? No. Some people test because of ongoing digestive symptoms; others are simply curious or want to be proactive. Either is fine — but if you have symptoms that concern you, see your GP as well.

Which test should I start with? If you're new to gut testing or want an affordable baseline, the Microbiome Check is a great start. If you want a thorough DNA-based picture with function and inflammation markers, the GI-MAP is ideal. For the deepest, most complete view, choose the Advanced Microbiome GutIQ.

Will the test tell me exactly what to eat? Not by itself. It gives insight into your gut community, which — combined with your goals and a practitioner's input — can help guide personalised choices. It isn't a prescriptive meal plan.

How often should I test? Many people test once for a baseline, then again after several months if they've made changes and want to see the effect. There's no need to test frequently.

Is the collection unpleasant? It's a simple at-home stool collection with clear instructions. Most people find it quick and straightforward.

What if a pathogen or parasite is found? Some findings need medical follow-up, and certain infections are notifiable to public health authorities by the lab. If something like this shows up, we'll point you toward appropriate next steps, and you should see your GP.

Can this replace advice from my doctor? No. It's an insight tool that complements medical care — it doesn't replace it. Always see your doctor for symptoms that need evaluation.

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Still deciding? Microbiome Check $239 · Complete Microbiome Mapping $569 · Advanced Microbiome GutIQ $599 · or the Platinum Gut Health Check (microbiome + food intolerance + leaky gut + SIBO)

Gut health is rarely one test's job. Depending on what you're exploring, these related i-screen tests and resources may help:

• Microbiome Check · Complete Microbiome Mapping (GI-MAP) · Advanced Microbiome GutIQ — the three microbiome tests compared above.
• SIBO Breath Test (Glucose + Lactulose) — for suspected small intestinal bacterial overgrowth (bloating, distension after meals).
• Intestinal Permeability (Leaky Gut) Test — a focused look at gut-barrier integrity.
• Food Intolerance (IgG) Test — an IgG screen across common foods for delayed-type food reactions.
• H. pylori Stool Test · Parasite PCR Test — targeted screens for specific organisms.
• Platinum Gut Health Check and Gut Health Test — comprehensive panels that combine several of the above.
• Nutrition Assessment — add a dietitian's review to turn your results into a plan.

Explore more: Improve Gut Health & Digestion · browse all tests · gut health articles · collection instructions · FAQ.

Your gut microbiome is one of the most influential systems in your body — and one you can actually get a clear look at. A microbiome test won't diagnose you or hand you all the answers, but it can give you and your practitioner a genuinely useful window into how your inner ecosystem is doing, and a practical starting point for looking after it well.

Whether you want a simple baseline or the deepest possible picture, there's an i-screen test to match — and support on hand to help you make sense of what it finds.

[NEW]

Order the Microbiome Check — $239 Order Complete Microbiome Mapping — $569 Order the Advanced Microbiome GutIQ — $599

Want a practitioner to walk you through the results? Add a Nutrition Assessment.

This guide is for general education and wellbeing. It is not medical advice and does not diagnose, treat, cure or prevent any condition. Always consult a qualified healthcare professional about symptoms or health concerns.