The Microbiome Clinic
Founded by Dr. Paul Froomes, Gastroenterologist

Doctors who address the root-cause.

We test what you can't see — then treat the root cause of chronic gut, skin, mood, and fatigue issues.

No referral needed · Telehealth Australia-wide
AHPRA-Registered
Microbiome Doctors™
Test. Repair. Maintain.™
Root-cause methodology
Telehealth Australia-wide
See a doctor from anywhere
4.9
21 reviews
Google Reviews
Meg Popple

The Microbine treatment has literally changed my life for the absolute best. If you’re suffering with any gut issues… contact Charlie and the incredible team at the Microbine Clinic as you won’t regret it.

Claudia Cox

Absolutely blown away by the support from the team at the Microbiome Clinic. From my first consultation, I felt genuinely heard, understood, and supported, and communication was amazing, I always got prompt same-day responses whenever I needed help. After trying many different treatments, and programs without real results, this is the first time I’ve experienced genuine improvement, and it’s made a huge difference. A huge thank you to Jackson and Charlie, who went out of their way to personally deliver my medication when I couldn’t organise it before heading away. It really shows how committed they are to their clients’ goals and the level of care they provide. Super impressed with the clinic would highly recommend!!

Diane Grech

I have Ankylosing Spondylitis (a form of arthritis), which I got in my early teens and I am now in my sixties. I have suffered with this disease for decades and undergone many joint replacements (hips, knees, ankle). Treatment has mostly been steroids to try and reduce the inflammation and opioids for pain relief. I had been in a lot of pain due to many swollen joints. I had difficulty walking and very low energy for quite a long time now. Both shoulders were very painful and had minimal movement. I was scheduled to see a shoulder surgeon to look into getting shoulder replacements. My quality of life was pretty awful.

Olivia Payne

I honestly can’t recommend the Microbiome Clinic enough. After struggling with gut issues for so long, I finally feel like myself again – my gut health has been genuinely life-changing. The process felt thorough, personalised, and easy to follow, and the support throughout made such a difference. I’m now in phase 2 of my treatment and feeling better than I ever have – symptoms I thought were just “normal” for me are completely gone. It’s such a relief to have clarity, a plan that actually works, and practitioners who truly listen. If you’re on the fence about getting your gut health sorted, this is 100% worth it.

Jacqui Elm

I am grateful to Dr Paul Froomes for his expertise and dedication to gut health. I consulted for both my adult children—one with Crohn’s (and using biologics for over 2 years, but never able to get a normal faecal calprotectin) and the other with IBS-like symptoms. Following gut microbiome mapping, we opted out of antibiotics but followed the protocol. Within five weeks, my child with Crohn’s saw faecal calprotectin drop from over 200 to 6 (normal range is under 50), without strict dietary changes. My other child, sceptical at first, also noticed improvements. Special thanks to Charlie, who was always efficient, caring, and responsive—even during holidays.

Tracey Smyth

After suffering for years with IBS and a recent diagnosis of coeliac disease, the Microbiome Clinic discovered the underlying causes and reset my gut. No more bloating, upset stomach or poor metabolism. My sleep has improved and my energy returning. I’m so happy with the results.

Christopher Downie

After 10+ years of stomach issues and debilitating pain, this is the best I have felt in a very long time. I have seen numerous GPs and specialists to no avail. I found Dr Froomes and The Microbiome Clinic through my own research. Taking the microbiome test and the supplements and diet recommended by Dr Froomes has made an enormous difference in the space of a month. I am very happy with the advice and information provided as well as the accessibility to answer any questions along the way. I have been vocally recommending this course of action to friends and family with similar conditions.

What we specialise in

For patients who've been dismissed, misdiagnosed, or told it's all in their head.

We're a medical clinic built for a specific kind of patient — the kind who's been living with unexplained symptoms for months or years, seen multiple doctors, done every test that comes back 'normal,' and been left without answers. We believe your symptoms are real. We find out why.

Your tests are all normal.
Every GP appointment
It's probably just IBS. Try managing your stress.
Gastroenterologist referral
There's nothing structurally wrong. It might be anxiety.
After a colonoscopy
Some people just have sensitive stomachs. You'll need to learn to live with it.
After years of appointments
We don't say any of those things.
We find out what's actually going on.
Root-Cause Medicine

What we treat

Chronic conditions linked to microbiome dysfunction — diagnosed and treated by specialists, not guesswork.

Gastroenterology

12 Conditions
  • IBS (Irritable Bowel Syndrome)
  • SIBO (Small Intestinal Bacterial Overgrowth)
  • Chronic Bloating & Gas
  • Constipation & Diarrhoea
  • Leaky Gut (Intestinal Permeability)
  • H. Pylori & Parasites

Skin & dermatology

6 Conditions
  • Acne (Hormonal & Cystic)
  • Eczema & Dermatitis
  • Rosacea
  • Psoriasis
  • Unexplained Rashes
  • Perioral Dermatitis

Mood & cognition

7 Conditions
  • Anxiety & Low Mood
  • Brain Fog
  • Chronic Fatigue
  • Depression (Gut-Brain Axis)
  • Poor Sleep & Insomnia
  • Stress-Related GI Symptoms

Gynaecological & urinary

5 Conditions
  • Recurrent Thrush (Candida)
  • Bacterial Vaginosis (BV)
  • Recurrent UTIs
  • Vaginal Dysbiosis
  • Post-Antibiotic Flora Disruption

Autoimmunity & inflammation

6 Conditions
  • Rheumatoid Arthritis
  • Ankylosing Spondylitis
  • Inflammatory Bowel Disease (IBD)
  • Chronic Joint Pain
  • Food Sensitivities & Allergies
  • Systemic Inflammation
+More
Root-cause microbiome medicine
Test. Repair. Maintain.

How it works

A clear, doctor-led process designed to find and fix the root cause — not just mask your symptoms.

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OK HIGH OK LOW

Test your microbiome

Speak to our patient care team to learn which tests our doctors recommend based on your specific symptoms.

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February 2026 M T W T F S 3 4 5 6 7 8 10 11 12 13 14 15 17 18 19 20 21 22 Dr. Froomes 10:30 AM · Telehealth

See a Microbiome Doctor™

Medical doctors and microbiome specialists who design a personalised program tailored to your clinical profile and diagnostic results.

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YOUR REPAIR PROGRAM The Microbiome Clinic™ 67% through repair phase

Repair your microbiome

Follow your personalised repair program and treat the root cause of your symptoms — not just manage them.

30-second quiz

Is The Microbiome Clinic right for you?

Answer 7 quick questions to find out whether our specialist approach is a fit for what you're experiencing.

1 of 7
Question 1 of 7
Have you been experiencing gut or digestive issues?
Bloating, constipation, diarrhoea, reflux, food intolerances, nausea, or abdominal pain.
Question 1 — follow-up
Which of these do you experience?
Select all that apply.
Question 2 of 7
Have you seen a GP or specialist about these symptoms?
And been told your tests are "normal," it's "just IBS," or to manage your stress.
Question 3 of 7
Have you been prescribed medications, put on restrictive diets, or given a host of random supplements — without any real system — that didn't work or made things worse?
When treatment isn't guided by proper testing, it's trial-and-error. That's not a plan — it's guesswork.
Question 4 of 7
Do your symptoms affect your daily life — what you eat, where you go, your energy, or your confidence?
Many patients don't realise how much they've adjusted their life around their symptoms until someone asks.
Question 5 of 7
Would you prefer a structured program with a clear plan and an end point — rather than ongoing appointments?
Test. Diagnose. Treat. Review. A defined pathway, not endless visits.
Question 6 of 7
Would you prefer to start with testing — rather than paying for an initial consultation first?
Our patient care team gets you set up with the right test immediately, at no extra cost.
Question 7 of 7
Do you want a medical doctor who actually listens to you, investigates deeper, and addresses the root cause — with a blend of medicine, supplements, and diet?
Not someone who writes a script in 10 minutes. A specialist who builds a plan around you.
Thanks! Our patient care team will be in touch shortly.
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Why us

Not a GP. Not a naturopath. Something better.

We combine the clinical authority of specialist medicine with the open-minded, whole-person approach that conventional care ignores — structured into a defined program with an end point, not endless appointments.

Standard care
Your GP
Generalist care across all conditions
Approach
Symptom management — limited time, limited scope
Microbiome expertise
No microbiome training — 6+ month gastro wait
Testing
Basic bloods and stool culture — misses most imbalances
Patient validation
"Your tests are normal" — dismissed as stress or IBS
Nutrition & lifestyle
"Eat more fibre, drink more water"
Treatment
PPIs, laxatives, antidepressants — symptom relief only
Cost & structure
Low per-visit cost but no program — no end point
Getting started
Book, wait 2–4 weeks, get a 10-minute slot
Goal
Manage symptoms — see you again next month
Recommended
The Microbiome Clinic™
Australia's first medical practice dedicated to the microbiome
Approach
Root-cause focused — identify what's driving symptoms and build a plan to resolve it
Microbiome expertise
Australia's only microbiome specialists — gastroenterologist, 25+ years experience
Testing
Advanced microbiome mapping — NATA-accredited qPCR across gut, oral, vaginal, and SIBO
Patient validation
We start by listening — your symptoms are real, not in your head
Nutrition & lifestyle
Western meets functional medicine — pharmaceuticals, nutrition, supplementation, and lifestyle
Treatment
Personalised protocols — targeted antimicrobials and dietary programs specific to your results
Cost & structure
Defined program with an end point — we don't want to keep you coming back
Getting started
No initial consult required — patient care team gets you started immediately
Goal
Resolve the problem — treat it, confirm it's gone, stay well
Alternative care
Naturopath
Holistic practitioner, non-medical
Approach
Holistic view but no medical framework — trial-and-error supplements
Microbiome expertise
Interested in gut health — cannot prescribe or diagnose
Testing
May order tests but interpretation varies — no clinical framework
Patient validation
Empathetic and willing to listen — validates patient experience
Nutrition & lifestyle
Strong on nutrition — but no prescribing authority
Treatment
Herbal protocols only — cannot prescribe when needed
Cost & structure
Expensive programs ($3k–$8k+) — ongoing costs, no end point
Getting started
Initial consult ($150–$300) before anything begins
Goal
Improve wellbeing — no objective testing to confirm resolution

Gut & SIBO Test Bundle
Gut & SIBO Test Bundle
Gut & SIBO Test Bundle
Gut & SIBO Test Bundle

Get to the root-cause.

Gut Health Testing Bundle

Includes Gut Microbiome Test & SIBO Breath Test — everything you need to uncover the root cause of your symptoms in one complete bundle.

Bloating Food Intolerance IBS Constipation Gas SIBO Fatigue Autoimmunity
70+ Bio Markers
Complete Gut Microbiome Test & SIBO Breath Test
At-home sample collection — no clinic visit needed
Results in 10-14 days
$ 670

Includes at-home sample collection kits with prepaid return shipping.

Start testing
Telehealth Australia-wide
Medical-Grade Diagnostics
Founding Gastroenterologist

Dr. Paul Froomes

Chief Medical Officer & Microbiome Pioneer

MBBS FRACP AGAF Gastroenterologist Hepatologist

Dr. Paul Froomes is a board-certified gastroenterologist and hepatologist with over 30 years of clinical experience. As one of Australia's leading microbiome specialists, he has personally treated more than 10,000 patient microbiomes — pioneering evidence-based protocols that target the root cause of chronic conditions, not just their symptoms.

TGA Accredited FMT Provider
Faecal Microbiota Transplant
Author of Your Best Gut
A microbiome memoir
30+ Years Practising
Board-certified specialist
Gastroenterologist & Hepatologist
FRACP, AGAF certified
Dr. Paul Froomes

Every chronic condition I see — IBS, skin issues, mood disorders — almost always traces back to the microbiome. Test it, and you can fix it.

— Dr. Paul Froomes

Our doctors do things differently.

The world's first dedicated microbiome clinic.

An online medical clinic built exclusively for the diagnosis and treatment of inflammatory and microbiome-linked illness. No generalists. No guesswork. Just specialists who understand your condition.

Evidence-backed Root-cause Microbiome Doctors™ Telehealth
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Common Questions

Everything you need to know

New to microbiome medicine? Here are the answers to questions we hear most from patients just like you.

Yes — every doctor at The Microbiome Clinic is a fully registered medical practitioner with AHPRA (the Australian Health Practitioner Regulation Agency). Our founding doctor, Dr. Paul Froomes, is a board-certified gastroenterologist and hepatologist with over 30 years of clinical experience, and a Fellow of the Royal Australasian College of Physicians (FRACP). These are the same qualifications required to practise in any Australian hospital.

Absolutely. The role of the gut microbiome in human health is one of the most active and well-funded areas of medical research in the world. Over 70,000 peer-reviewed studies have been published on the human microbiome, with major research from institutions including Harvard, Stanford, the Weizmann Institute, and Australia's own CSIRO. Conditions like IBS, IBD, eczema, depression, autoimmunity, and metabolic disease have all been clinically linked to microbiome dysfunction. We don't practise alternative medicine — we practise evidence-based medicine with a specialist focus on the microbiome.

Consultations with our Microbiome Doctors are private specialist appointments and are not currently bulk-billed through Medicare. However, if you have a referral from your GP to see Dr. Paul Froomes specifically, you may be eligible for a partial Medicare rebate as a referred specialist consultation. Our patient care team can walk you through the costs before you book — there are no hidden fees.

No — you do not need a GP referral to book a consultation with our Microbiome Doctors or to order any of our testing kits. You can self-refer and get started straight away. The one exception is if you'd like to see Dr. Paul Froomes directly for a specialist gastroenterology consultation — in that case, a GP referral is required (and also allows you to access a Medicare rebate). If you're unsure which pathway is right for you, book a free discovery call and our patient care team will guide you.

All consultations are conducted via secure video call — you can see your doctor from anywhere in Australia, from the comfort of your own home. After booking, you'll receive a link to join your appointment at the scheduled time. Your doctor will review your test results, medical history, and symptoms, then design a personalised treatment program. Follow-up appointments, pathology reviews, and ongoing care are all handled through telehealth as well.

Most microbiome test results are returned within 2–3 weeks from the time the lab receives your sample. SIBO breath test results are typically faster, around 5–7 business days. Once your results are in, our team will contact you to book a results consultation with your doctor, who will walk you through every finding and your personalised treatment plan.

We specialise in chronic conditions linked to microbiome dysfunction, including IBS, SIBO, chronic bloating, inflammatory bowel disease (IBD), eczema, acne, rosacea, anxiety, brain fog, chronic fatigue, recurrent thrush, bacterial vaginosis (BV), UTIs, autoimmune conditions, and food sensitivities. If you've been told your symptoms are "just stress" or "normal" — they're not, and we can help. See our full conditions list.

We are a registered medical clinic, not a naturopathic or alternative health practice. Our doctors hold specialist medical qualifications (FRACP, MBBS) and are regulated by AHPRA — the same body that regulates every doctor in Australia. We use diagnostic-grade laboratory testing (not unvalidated food sensitivity panels), evidence-based treatment protocols, and pharmaceutical-grade interventions where clinically indicated. Think of us as specialist medicine with a microbiome focus, not wellness with a medical label.