As a medical naturopath (ANPA registered), nutritionist, herbalist and mental health specialist (PACFA registered), I help people from all over the world, who are considering a fecal microbiota transplant. I am scientifically; university trained and use science informed approaches, having studied gut health for many years. You may qualify for healthfund rebates.
The living commensal bacteria (friendly) bacteria in our gut sometimes get damaged. The dangerous pathogenic (harmful) bacteria can then take over and cause sever life threatening illness.
The damage to the gut can include small bowel intestinal overgrowth (SIBI), ulcerative colitis, Crohn’s disease, irritable bowel syndrome, chronic constipation, cramping, vomiting, bloating and diverticulitis
This may be due to many different kinds of bacterial viral, fungal, and nematode infestation. In some cases, you may have multiple pathogenic life-threatening infections. (1)
What Is fecal microbiome transplant (FMT)?
It’s when a portion of one healthy person’s fecal matter is taken and transplanted into a sick person, who has a damaged gut microbiome (the bacterial composite of the gut).
The microbiome is living balance of microbes in your gut that supports every system of your body. At times when it’s damaged you are unable to rebalance that mixture of microbes naturally.
When a healthy person’s fecal matter, containing a healthy level of gut microbes, is transplanted into your gut it can rebalance the microbiome and restore wellness.
It might sound very simple, but it is also very effective with no side effects if done correctly, and I emphasise the importance of this procedure being scientifically executed. (2)
Am I suitable for fecal microbiome transplant?
One of the early problems is that you may see your symptoms as only temporary. Your health practitioner may also not be taking your symptoms seriously and give you the wrong medication simply to get you out of the consultation room so they can get onto the patient.
Eubiosisis is when the friendly and pathogenic bacteria in your gut are balanced creating health. Gut dysbiosis is when the balance of good bacteria and bad bacterium in your gut is unbalanced, which always leads to illness. Not just slight illness health but also long-term life-threatening illness. (3)
Many health practitioners are not trained in gut health, or it’s effects on your general physical and mental health.
Testing for microbiome damage
In seeing you as patient I regularly order many tests to analyse the bacterium and other microbic profiles in your gut. There is no room for guess work as we must have clear facts from laboratory analysis and reports to see what is happening to your gut.
Whilst blood tests may give us some general information about infections, inflammation or organs damage, they are not enough. I may dig deeper into data via ordering fecal matter testing, genomic fecal matter profiling for pathogens like, Clostridioides difficile (C. diff), Klebsiella, viral gastroenteritis, norovirus or rotavirus, viral gastroenteritis, often called the “stomach flu”. It is an inflammation of the stomach and intestines caused by viruses like norovirus (most common in adults) and rotavirus.
I may also order organic acid urine test where I can see there has been mitochondrial damage to your system. (4) Mitochondria is the energy machine of all your cells, when gut is damaged so in the is ti s energy production. The leads to failure to heal and chronic fatigue syndrome (CFS).
Toxicology and health metals
The world is a poisonous place, danger is present everywhere, but often we do not see how dangerous it can be. Your body, however, does record its exposure to detrimental and toxic substances that damage the bacteria in your bowel and create poor health.
There may be heavy metals traces in your hair, body or lymph nodes. By testing for these potentially lethal heavy metal or toxics substances it gives us an indicator of your need to detox in order to restore your gut health.
You may have been exposed to toxins in the home or workplace that have been stored in your bones or lymph nodes that are slowly being released into the body and continually damage your gut microbiome. (5)
Again, it is important to remember that most medical practitioners do not test for these toxins, nor do they understand how symptoms you are showing relate to that toxic load.
Gut damage due to pathogen exposure
Often when I see patients in the clinic with gastrointestinal problems, who are unable to identify at what point they became ill.
All they seem to know is that their gut has not been right for long time and they’re not sure if the other symptoms they show are connected.
You can pick up pathogenic gut microbes from anyone and anywhere. This is particularly true if you have been to another country, had diarrhea or stomachache and later developed gut problems.
Some of these pathogens we can identified by laboratory testing but some we cannot yet detect. We can, however, see the effects that these infections can have on your gut and general health.
In these cases, as a medical herbalist, I treat they infections herbily in order to kill them but not damage your microbiome and gut further.
Drug and medication damage to your microbiome
One of the major causes of gut dysbiosis is the side effects of medication. It may have been at prescription or a treatment you had decades ago.
Your medical practitioner may also refuse to acknowledge this damage for two reasons. The first is that they aren’t trained to recognise these symptoms at medical school. The second it if they acknowledged it was a medication side effect it also leaves them open to being sued for malpractice.
The research tells us that the common medication side-effects are from the administration of antibiotics. Again, that could be prescription you were given decades ago. (6)
When this is identified people and doctors simply do not believe you that they may blanketly refuse to acknowledge that damage is connected with a prescription. You get classified as the dilutional, ill-informed and a difficult patient.
Fecal microbiota transplant and mental health
Your gut health affects all the system in your body including your mental health and moods. Research now shows us that poor gut health can lead to psychiatric illness and anxiety, depression, bipolar disorder and psychosis. (7)
The gut/brain axis is where the microbiota in your gut controls your hormonal levels like insulin, glycogan, cortisol, catecholamines, serotonin, endophorias, dopamine and melatonin. Damage to the gut and dysregulation of hormonal levels leads to mental illness all of kinds.
Research now showed us fecal microbiome transplant can reverse see mental illness in many patients quite miraculously disappearing so there no longer need psychiatric medication.
Is fecal microbiota transplant safe?
Yes, but only if it is done correctly with professional health care guidance. (8) There are many medical screening processes of both the recipient and the donors that must go through. I myself had an FMT when I became violently ill with a life threatening illness after a doctor had mis prescribed me the wrong medication.
In choosing my treatment I screened many clinics throughout the world for their doner and treatment processes. It was utterly shocked at how inadequate many clinics and laboratories were in producing samples for a fecal microbiome transplant. Many, who were even government registered, refused to fully disclose their screening process. Some clinics and laboratories lied about the way they were cutting condors on donor testing.
It was only because I had scientific training that I was able to eventually find a source of donor which I felt safe with that resulted in successful treatment.
So, the answer is ‘Yes’, fecal microbiome transplant is safe when done correctly under health care supervision and advice.
How much is fecal is fecal microbiota transplant?
This depends on where you are and what method of transplant you choose. Costs can run from the equivalent of USA$5000 to over USA $100,000.
There is no relation between higher priced treatments and better results. What is important is for you to have the right information on the method used for your condition and whether the facility can provide quality donor products.
Do not – and I repeat do not try this at home without consulting a health care professional. It could expose you to further infection which could end up being life threatening.
As well as the cost of the process, there will also be many laboratories screening processed you will need to go through. Do not miss these to save costs.
That of course might not cure all of your medical problems. You may still be left with damage that the original biological insult on your gut caused, known as a secondary illness. I can also help you look at ways to deal with these extended health issues.
How to choose the right FMT
My job is to help you diagnose the problem and guide you towards the right treatment and facility that is appropriate for you. That does not mean the easiest option but the choice that will give you best results.
The procedure can be delivered by colonoscopy, enema, nasal gastric tube, swallowed fluid or capsules. All have been shown to be affective.
Once we have all the laboratory results in, only then we will discuss your options. I support through the whole process from beginning to end.
That support includes:
- The correct testing
- Choosing the right method
- Finding the right facility
- How to kill the unwanted pathogen
- What you need to eat
- How you need to rebuild your gut microbiota
- Mental health support
- Working with your budget
Dr Tracie O’Keefe is medical naturopath, nutritionist, herbalist and mental health professional. She works with and has a great interest in gut health and the use of fecal microbiota transplant to restore gut health and wellbeing. Call Australia 0403 398808 now. In clinic visits or via the internet from anywhere in the world.
References
(1) de Vos, W. M., Tilg, H., Van Hul, M., & Cani, P. D. (2022). Gut microbiome and health: Mechanistic insights. Gut, 71(5), 1020–1032. https://doi.org/10.1136/gutjnl-2021-326789
(2) Novelle, M. G., Naranjo-Martínez, B., López-Cánovas, J. L., & Díaz-Ruiz, A. (2025). Fecal microbiota transplantation, a tool to transfer healthy longevity. Ageing Research Reviews, 103, Article 102585. https://doi.org/10.1016/j.arr.2024.102585
(3) Shen, Y., Fan, N., Ma, S.-X., Cheng, X., Yang, X., & Wang, G. (2025). Gut microbiota dysbiosis: Pathogenesis, diseases, prevention, and therapy. MedComm, 6(5), Article e70168. https://doi.org/10.1002/mco2.70168
(4) Bautista, J., & López-Cortés, A. (2026). Mitochondrial drivers of stem cell aging and inflammaging. npj Aging. https://doi.org/10.1038/s41514-026-00422-5
(5) Ibarra-Mendoza, B., Gomez-Gil, B., Betancourt-Lozano, M., Raggi, L., & Yáñez-Rivera, B. (2023). Microbial gut dysbiosis induced by xenobiotics in model organisms and the relevance of experimental criteria: A minireview. Gut Microbiome, 4, Article e7. https://doi.org/10.1017/gmb.2023.3
(6) Baldanzi, G., Larsson, A., Sayols-Baixeras, S., Dekkers, K. F., Hammar, U., Nguyen, D., Graells, T., Ahmad, S., Gazolla Volpiano, C., Meric, G., Järhult, J. D., Tängdén, T., Ludvigsson, J. F., Lind, L., Sundström, J., Michaëlsson, K., Ärnlöv, J., Kennedy, B., Orho-Melander, M., & Fall, T. (2026). Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals. Nature Medicine, 32, 1351–1361. https://doi.org/10.1038/s41591-026-04284-y
(7) Grau-Del Valle, C., Fernández, J., Solá, E., Montoya-Castilla, I., Morillas, C., & Bañuls, C. (2023). Association between gut microbiota and psychiatric disorders: A systematic review. Frontiers in Psychology, 14, Article 1215674. https://doi.org/10.3389/fpsyg.2023.1215674
(8) Karimi, M., Shirsalimi, N., Hashempour, Z., Salehi Omran, H., Sedighi, E., Beigi, F., & Mortezazadeh, M. (2024). Safety and efficacy of fecal microbiota transplantation (FMT) as a modern adjuvant therapy in various diseases and disorders: A comprehensive literature review. Frontiers in Immunology, 15, Article 1439176. https://doi.org/10.3389/fimmu.2024.1439176
