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.
Trusted by Australians. Led by Doctors.
Real stories from real patients who've transformed their health through evidence-based microbiome medicine.
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.
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!!
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.
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.
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. I was referred to Dr Froomes as my liver function blood tests were not looking very good. At the initial consultation, Dr Froomes asked me questions regarding my bowel. He then conducted blood tests and stool sample tests. He found there were very bad microbiome in my bowel and no good microbiome at all. Dr Froomes recommended the 4 week Gut Repair Program, Faecal Microbiome Transplants (FMT), followed by the Gut Maintenance Program. I was extremely sceptical and it wasn't going to be cheap. However, being in so much pain all over, and with no energy I had no choice but to try this. It has now been 10 weeks and I am truly amazed with the results. This treatment has been life changing! The changes I have seen are: - Reduction of swelling in many joints - Drop in overall Pain Levels - Increase in Energy Levels - Bowel is more regular and no bloating - Inflammation Levels have dropped significantly, blood tests have confirmed this - Ability to walk much more comfortably and for longer distances - Shoulder pain reduced significantly - Increased mobility in many joints, including the shoulders. With my body now on the road to recovery, I have now been able to: - Reduce steroid and opioid intake - Cancel shoulder surgeon's appointment Dr Froomes is such a lovely man to deal with and always made me feel very comfortable. All his staff that I have dealt with are just as lovely too. I only wish I had done this years ago. I now feel I have my life back. Thank you Dr Froomes for everything you have done for me. I cannot believe how far I have come. I do not usually post reviews, but I wanted to highly recommend anybody who has arthritis to do this Gut Repair Program, as it truly does work!!
What we treat
Chronic conditions linked to microbiome dysfunction — diagnosed and treated by specialists, not guesswork.
Gastroenterology
- IBS (Irritable Bowel Syndrome)
- SIBO (Small Intestinal Bacterial Overgrowth)
- Chronic Bloating & Gas
- Constipation & Diarrhoea
- Leaky Gut (Intestinal Permeability)
- H. Pylori & Parasites
Skin & dermatology
- Acne (Hormonal & Cystic)
- Eczema & Dermatitis
- Rosacea
- Psoriasis
- Unexplained Rashes
- Perioral Dermatitis
Mood & cognition
- Anxiety & Low Mood
- Brain Fog
- Chronic Fatigue
- Depression (Gut-Brain Axis)
- Poor Sleep & Insomnia
- Stress-Related GI Symptoms
Gynaecological & urinary
- Recurrent Thrush (Candida)
- Bacterial Vaginosis (BV)
- Recurrent UTIs
- Vaginal Dysbiosis
- Post-Antibiotic Flora Disruption
Autoimmunity & inflammation
- Rheumatoid Arthritis
- Ankylosing Spondylitis
- Inflammatory Bowel Disease (IBD)
- Chronic Joint Pain
- Food Sensitivities & Allergies
- Systemic Inflammation
Beyond a Blood Test.
Years of unexplained symptoms deserve more than another Google search. DNA-based microbiome testing reveals exactly what's driving your condition — so we can fix it at the root.
Gut Microbiome Test
Comprehensive DNA analysis of your gut bacteria, fungi, and parasites. The same test trusted by gastroenterologists to identify the root cause of chronic digestive issues.
Oral Microbiome Test
Your mouth is the gateway to your gut. DNA profiling of your oral bacteria reveals hidden drivers of gum disease, bad breath, and systemic inflammation — before they become bigger problems.
Vaginal Microbiome Test
Stop the revolving door of antibiotics and antifungals. DNA profiling reveals the specific bacterial imbalance driving recurrent thrush, BV, and UTIs.
How it works
A clear, doctor-led process designed to find and fix the root cause — not just mask your symptoms.
Test your microbiome
Speak to our patient care team to learn which tests our doctors recommend based on your specific symptoms.
See a Microbiome Doctor™
Medical doctors and microbiome specialists who design a personalised program tailored to your clinical profile and diagnostic results.
Repair your microbiome
Follow your personalised repair program and treat the root cause of your symptoms — not just manage them.
Get started today.
Speak to our patient care team to find out which tests and programs are right for your symptoms. No obligation, no pressure.
Dr. Paul Froomes
Chief Medical Officer & Microbiome Pioneer
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.
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 FroomesGet 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.
Includes at-home sample collection kits with prepaid return shipping.
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.
Everything you need to know
New to microbiome medicine? Here are the answers to questions we hear most from patients just like you.
Book a free discovery call or email us at reception@themicrobiomeclinic.com.au
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.