A gut microbiome test uses DNA from a stool sample to identify the organisms living in the bowel. Nutripath’s Complete Microbiome Mapping uses targeted PCR plus stool markers such as calprotectin and pancreatic elastase. The Advanced version adds culture and sensitivity testing, GutIQ uses shotgun metagenomic sequencing across 28,000+ species, and there are versions for babies and children. There is no agreed healthy microbiome, so results guide a plan rather than give a diagnosis. Verified practitioners can order these kits through Vively.
| Test type | Measured in a stool sample |
|---|---|
| Nutripath code | 2206, 2211, 2207, 2212, 2217, 2218 |
| Sample and collection | Stool kit collected at home and posted to Nutripath |
| Preparation | Eat as usual. Ideally wait 4 weeks after antibiotics and 2 weeks after antifungals, and check with the prescriber before pausing medicines. Don’t collect during a stomach bug. |
| Turnaround | 5 to 10 business days depending on the version (Nutripath estimates, from when the lab receives the sample). Allow extra days for postage. |
| Available through | Nutripath test ordered through Vively. You need to be a verified practitioner to refer it. |
| Pricing | Pricing in your practitioner account |
| Results | PDF report from Nutripath, filed in your client’s record and app beside their blood results |
Only practitioners can order this test. Ask your naturopath, nutritionist or dietitian whether they use Vively.
What do Nutripath’s microbiome tests measure, and how do the options differ?
All six use one stool sample collected at home. They differ in how the organisms are identified and how many stool markers come with them.
Quantitative PCR for a set list of beneficial bacteria, opportunistic organisms, pathogens, yeasts, parasites and viruses, with faecal markers including calprotectin, pancreatic elastase, secretory IgA, zonulin, beta-glucuronidase, occult blood and anti-transglutaminase IgA.
The same PCR panel plus culture of organisms that grow, tested against medicines and natural agents, and short chain fatty acids. Useful when you want to know what a cultured organism responds to.
The PCR organism panel on its own. Nutripath positions it as a follow-up test after a full mapping.
Sequences all the DNA in the sample and reports from a library of 28,000+ species, with stool markers, short chain fatty acids and pH. It gives a broader view but more data to interpret.
Metagenomic tests read against age-specific reference ranges: BabyBiome for ages 0 to 3 and PaediatricBiome for ages 3 to 17.
| Nutripath test | Code | Sample | Turnaround |
|---|---|---|---|
| Complete Microbiome Mapping | 2206 | Stool | 7 to 10 business days |
| Advanced Complete Microbiome Mapping and Microbial Sensitivities | 2211 | Stool | 5 to 7 business days |
| Microbiome Basic | 2207 | Stool | 5 to 7 business days |
| Microbiomix Metagenomic Mapping | 2212 | Stool | 7 business days |
| BabyBiome GutIQ (ages 0 to 3) | 2217 | Stool | 7 business days |
| PaediatricBiome GutIQ (ages 3 to 17) | 2218 | Stool | 7 business days |
How do you order a gut microbiome test through Vively?
- Get verified. You need to be a verified practitioner to refer tests. Practitioners with a recognised qualification or membership (ATMS, NHAA, ANTA, Dietitians Australia, NSA, CMA or Ahpra registration) can request free practitioner access.
- Build the order. Log in to the practitioner platform, choose the Nutripath test and add any blood tests or the $99 Baseline Health Check to the same order. Pricing shows in your account, and either your client or your practice can pay.
- Client collects at home. Nutripath sends your client the collection kit once the order is placed. Your client follows the kit instructions (a small amount of one stool sample into the tubes provided) and posts the sample back to Nutripath in the packaging provided.
- Review the report. Nutripath’s PDF report is filed in your client’s record and app, next to their blood results, ready for the follow-up consult.
See every Nutripath test you can order on the Nutripath tests page.
Order a gut microbiome test with your client’s blood tests
Free access for verified naturopaths, nutritionists and dietitians. Order Nutripath tests and blood pathology in one place, and see every result in your client’s record.
What can a microbiome test tell you, and what can it not?
Stool microbiome tests can find pathogens and parasites and give a broad view of gut ecology. Using them to guide treatment in people without a clear infection is still an emerging area.
An international consensus statement found there is not enough evidence to support routine microbiome testing in clinical practice outside research, and called for better standards and reporting (Porcari et al., 2025).
Healthy people carry very different microbiomes, shaped by diet, age, medicines and where they live, so there is no single healthy profile to compare against (Shanahan et al., 2021).
Bacterial counts shift with diet, transit time and stool consistency, so two samples a few weeks apart can differ (Vandeputte et al., 2021). Look for large, consistent findings rather than small shifts.
A microbiome result cannot rule bowel disease in or out. Calprotectin, occult blood and red flag symptoms still decide who needs a GP and a colonoscopy.
How does a microbiome test fit with blood work?
Read the stool markers with a few blood results from the same order. They show whether gut findings are affecting absorption or inflammation, and whether a referral is needed.
- ReferRaised calprotectin or occult blood on the stool markers
Possible inflammation or bleeding in the bowel. Refer to the GP with the report before starting a gut protocol.
- ReferA parasite or pathogen such as Giardia, Cryptosporidium or C. difficile toxin
These can need medical treatment. Send the result to the GP, especially if the client has diarrhoea, fever or weight loss.
- ContextLow pancreatic elastase with low B12, iron or vitamin D
Poor digestion of fat and protein can reduce absorption. A low elastase needs GP follow up, and deficiencies should be confirmed and treated.
- ContextLow diversity or few beneficial bacteria, normal stool markers and blood count
A common finding after antibiotics or a low fibre diet. Work on fibre, plant variety and fermented foods, and retest only if it will change the plan.
What can affect a microbiome result?
- Antibiotics or antifungals in the past 4 weeks
- Probiotics, prebiotics and fibre supplements
- Proton pump inhibitors, laxatives and anti-diarrhoeal medicines
- A recent change in diet, travel or a stomach bug
- Stool consistency, hydration and how long the sample took to reach the lab
When should you refer the client to their GP?
- Raised calprotectin, positive occult blood or an anti-transglutaminase IgA result above the range
- A pathogen or parasite detected in a client with symptoms
- Rectal bleeding, black stools, unexplained weight loss or night time diarrhoea
- Iron deficiency anaemia or a change in bowel habit over the age of 45
- Any baby or child with poor growth, blood in the stool or ongoing diarrhoea
How should a client prepare for a gut microbiome stool test?
Copy or print this to send to your client. Follow the instructions in the Nutripath kit if they differ.
Preparing for your gut microbiome stool test
- Eat as you normally do in the days before the test.
- If you have taken antibiotics or antifungals recently, tell your practitioner. Testing is usually best 4 weeks after antibiotics.
- Ask your practitioner whether to pause probiotics or gut supplements before collecting. Don’t stop prescribed medicines without asking your doctor.
- Don’t collect during a stomach bug, while you have your period, or if you have bleeding haemorrhoids.
- Collect one stool sample at home using the kit Nutripath sends you, and fill the tubes as the kit describes.
- Post the sample back the same day, early in the week so it isn’t in the post over the weekend.
- Your practitioner will receive the report and go through it with you.
What does the microbiome mapping report look like?
Nutripath publishes sample reports on its website. They open in a new tab.
- Complete Microbiome Mapping sample report (PDF)
- Advanced Complete Microbiome Mapping and Microbial Sensitivities sample report (PDF)
- Microbiome Basic sample report (PDF)
- Microbiomix Metagenomic Mapping sample report (PDF)
- BabyBiome GutIQ (ages 0 to 3) sample report (PDF)
- PaediatricBiome GutIQ (ages 3 to 17) sample report (PDF)
How do practitioners use microbiome tests with clients?
They are most useful for a client with ongoing gut symptoms where a pathogen or parasite would change the plan, or after repeated antibiotics. Choose Complete Microbiome Mapping for a first test with stool markers, the Advanced version when you need sensitivities, GutIQ for a broader species view, and the children’s GutIQ tests for babies and kids. Check the stool markers first, refer anything that points to inflammation, bleeding or infection, and base the plan on large, consistent findings.
Complete Microbiome Mapping FAQs
Can a naturopath, nutritionist or dietitian order a gut microbiome test through Vively?
Yes. You need to be a verified practitioner to refer it. Add a Nutripath microbiome kit to an order in the Vively practitioner platform, on its own or with blood tests. Pricing shows in your account. No account yet? Request free access.
Which Nutripath microbiome test should I order?
Complete Microbiome Mapping suits most first tests. Choose the Advanced version if you want culture and sensitivity results, GutIQ for shotgun sequencing across thousands of species, Microbiome Basic as a follow-up organism panel, and BabyBiome or PaediatricBiome GutIQ for children.
Is a stool test the same as a gut microbiome test?
Not always. A gut microbiome test is one kind of stool test that maps the organisms in the sample. Other stool tests answer narrower questions, such as calprotectin for bowel inflammation or a CDSA for digestion markers. Choose the test by the question you want answered.
What is the difference between PCR and metagenomic microbiome tests?
PCR tests look for a set list of organisms and measure how much of each is there. Shotgun metagenomic sequencing reads all the DNA in the sample, so it finds more species but produces more data that is harder to interpret.
Can a microbiome test diagnose IBS or IBD?
No. IBS is diagnosed on symptoms once other conditions are ruled out, and IBD needs a doctor and usually a colonoscopy. The calprotectin marker on most of these tests helps decide who to refer.
How long do microbiome results take?
Nutripath estimates 5 to 10 business days depending on the version, from when the lab receives the sample. Allow extra time for postage.
References
- Porcari S, Mullish BH, Asnicar F, et al. International consensus statement on microbiome testing in clinical practice. Lancet Gastroenterology and Hepatology. 2025;10(2):154-167.
- Shanahan F, Ghosh TS, O’Toole PW. The healthy microbiome: what is the definition of a healthy gut microbiome? Gastroenterology. 2021.
- Vandeputte D, De Commer L, Tito RY, et al. Temporal variability in quantitative human gut microbiome profiles and implications for clinical research. Nature Communications. 2021.
- Nutripath. Complete Microbiome Mapping (2206), Advanced (2211), Microbiome Basic (2207), GutIQ (2212), BabyBiome GutIQ (2217) and PaediatricBiome GutIQ (2218). nutripath.com.au, checked 1 October 2026.