When gut testing becomes part of the picture
Standard pathology does a reasonable job of ruling things out. It will tell you whether you have coeliac disease, whether your inflammatory markers are elevated, whether there’s overt blood in your stool. What it doesn’t tell you is what’s living in your gut, whether those organisms are producing the compounds your body needs, whether your intestinal barrier is compromised, or whether the microbial environment is contributing to your symptoms.
That gap is where microbiome analysis becomes clinically useful.
The gut microbiome — the community of bacteria, fungi, and other microorganisms living in your digestive tract — influences far more than digestion. It’s involved in oestrogen metabolism, immune regulation, neurotransmitter production, inflammation, and metabolic function. In midlife women, these connections are directly relevant. The oestrobolome — the subset of gut bacteria responsible for metabolising and recirculating oestrogens — becomes clinically significant when hormonal balance is already under strain.
When symptoms aren’t responding as expected, or when the clinical picture suggests the gut is part of the driver, microbiome testing gives us a clearer view of what we’re working with.
Microbiome analysis may be relevant if
- You’re experiencing bloating, reflux, constipation, diarrhoea, or abdominal discomfort
- Your pathology markers suggest possible infection, parasites, or gut inflammation
- You have hormonal symptoms that may have a gut-ecology component — including symptoms associated with perimenopause, PMOS, or endometriosis
- Your skin, immune function, energy, or mood symptoms appear connected to gut health
- You’ve had recent antibiotic use and want to understand your recovery
- Your gut symptoms are persistent, changed, or worsening despite dietary and supplement interventions
- You want a detailed, evidence-based picture of your microbiome before beginning a targeted gut restoration protocol
About Microba testing
Microba is an Australian clinical microbiome testing company. Simply Naturopathics is a Microba Clinical Partner, providing access to clinical-grade testing, practitioner-level reporting, and ongoing professional development in microbiome health.
The Microbiome Explorer range uses metagenomic next-generation sequencing (mNGS) to analyse the full spectrum of gut microbial species, not just those a targeted test was designed to look for. This distinction matters clinically: standard PCR-based stool tests identify what you’re testing for; mNGS identifies all microbial genetic material present in the sample. When symptoms are complex or unexplained, the difference is significant.
The Microba laboratory is ISO 15189-accredited. Results are measured against a healthy reference model and include an expert summary written by Microba’s clinical team, alongside evidence-graded insights across diet, lifestyle, and supplementation.
Microba offers three tiers of the Microbiome Explorer range. Pricing is confirmed and payment is handled directly through Microba when the test is ordered at your consultation.
All tests are available to adults 18 years or older. Testing is available to new and existing clients.
A note on what this testing does and doesn’t tell us
Microbiome analysis is a clinical tool. It informs naturopathic recommendations; it doesn’t diagnose a specific condition or replace conventional medical investigation where indicated.
Results are always interpreted in the context of your full clinical picture, including your symptom history, existing pathology, and current treatment plan. If your results suggest something that warrants referral or further investigation by your GP, I’ll say so.
Frequently asked questions
Do I need to have a consultation before I can order microbiome testing?
Yes. Testing is ordered through a consultation — either an Initial Clinical Assessment or a follow-up if you’re already an existing client. This is deliberate. The Microba report is a detailed clinical document that needs to be interpreted in the context of your full health picture, not read in isolation. Ordering the test without that clinical framework limits its usefulness considerably. If you’d like to discuss whether testing is appropriate for your situation, a Clarity Call is a good starting point.
How is this different from a standard stool test ordered by my GP?
Standard stool tests ordered in conventional medicine use targeted PCR-based technology. They identify specific pathogens the clinician is looking for, which means they’re only as useful as the clinical hypothesis behind the request. Microba’s Microbiome Explorer range uses metagenomic next-generation sequencing, which sequences all microbial genetic material in the sample. This means it identifies what’s present regardless of what was suspected. That’s a meaningful difference when symptoms are complex or haven’t been explained by standard investigation.
Can microbiome analysis help with hormonal symptoms in perimenopause, post-menopause, PCOS, or endometriosis?
In my clinical experience, gut ecology is an underappreciated factor in hormonal balance. The oestrobolome — the community of gut bacteria responsible for metabolising and recirculating oestrogens via the enterohepatic circulation — directly influences circulating oestrogen levels. When microbial diversity is reduced, beta-glucuronidase activity falls, which means oestrogens are less efficiently deconjugated and recirculated. This can affect circulating oestrogen levels whether the underlying condition is menopause, PMOS, or endometriosis.
This connection runs in both directions. Low oestrogen states (such as post-menopause) reduce gut microbial diversity, and a disrupted microbiome compounds the hormonal imbalance. In hyper-oestrogenic conditions such as PMOS and endometriosis, impaired microbial clearance of oestrogen can contribute to the excess circulating oestrogen that drives symptoms. Microbiome testing gives us a picture of where gut ecology sits in that cycle for you specifically.
A narrative review of the oestrogen-gut microbiome axis found that reduced gut microbiota diversity decreases oestrogen metabolism due to a lack of oestrogen-metabolising bacteria, and that specific microbial taxa are directly associated with urinary oestrogen metabolite profiles (e.g. DUTCH test) in women (Baker et al., 2017).
Baker, J. M., Al-Nakkash, L., & Herbst-Kralovetz, M. M. (2017). Estrogen–gut microbiome axis: Physiological and clinical implications. Maturitas, 103, 45-53. https://doi.org/10.1016/j.maturitas.2017.06.025
What happens if the results identify a pathogen or parasite?
If the Comprehensive panel identifies a pathogen or parasite, this will be clearly flagged in the report and discussed at your results review appointment. Depending on what’s found, management may fall within naturopathic scope, may require referral to your GP for medical treatment, or may involve a collaborative approach. I’ll be direct with you about which path is appropriate based on what the results show.
How long does the whole process take from ordering to results review?
Allow approximately five to six weeks from the time you complete payment through to your results review appointment. Kit dispatch takes 24-48 hours from payment. Sample return and laboratory processing takes approximately four weeks. Add time for booking your results review appointment once results arrive. If you’re working to a timeframe, factor this in when deciding when to order.
Does this test require any preparation?
Yes. Wait at least one month after completing a course of antibiotics or antimicrobials before collecting your sample. Antibiotic use significantly alters gut microbial composition, and recovery may take longer than four weeks in some cases. The collection guide covers all preparation requirements in detail. If you’ve recently completed antibiotics, let me know at your consultation and we’ll plan the timing accordingly.
You can find me in person, and online across Australia
In person —
Rutherglen, VIC
74 Main Street,
Rutherglen VIC
Wednesday, Thursday
In person — Yarrawonga, VIC
31-33 Belmore Street, Yarrawonga VIC
Friday
Telehealth
Available to clients anywhere in Australia.
All consultation types are available via telehealth during the Rutherglen hours.
All appointments are booked online. Full prepayment is required.
A 48-hour cancellation and rescheduling policy applies.
If your symptoms aren’t fully explained, or your gut function has changed in ways that haven’t responded to standard approaches, microbiome analysis may give us a more complete picture to work from. Book an Initial Clinical Assessment to discuss whether testing is the right next step for your presentation.
If you’re not sure whether this is the right fit, the Clarity Call is a good place to start. It’s ten minutes by phone, no obligation.
For more on how gut health connects to hormonal symptoms in midlife, see the Conditions page. For information on other specialist testing available at Simply Naturopathics, see Work with Tania.