FMT Procedure


Once you have selected to commence an FMT program you will be given a schedule and preparation instructions by the clinic FMT nurse. Prior to commencing FMT you will follow our dietary recommendations and take a course of specific antibiotics designed to target dysbiotic gut bacteria.


This will wipe clean the populations of bad bacteria that have overgrown your gut and are inducing illness. Once this is completed your gut will be full prepared to accept the complete new healthy microbiota form the FMTs. 


If you are doing your first FMT via colonoscopy you will take a bowel preparation the day prior to the colonoscopic FMT and present to the day centre fasting fro midnight the night before. For the entire day prior you will drink only clear fluids, like water, beef or chicken stock soup and jelly. You will take a sachet of picosolax in a glass of water at 3pm, then 1 litre of Gylcoprep C at 4 pm and finally another sachet of picosolax in a glass of water at 5 pm. 


There is no need for any fasting or bowel preparation prior to FMT enemas. They are designed to be self administered once our nurse has instructed you in how to do this.



It is recommended that you follow a LOW FIBRE DIET for 2 weeks prior to your first FMT and during the course of you antibiotics.


This will begin to starve out the bad bacteria that have overgrown your gut microbiome.


The following list gives you an idea of low fibre foods to eat:

  • meat - chicken, turkey, beef, lamb
  • fish - white fish, tune, salmon
  • milk, butter, olive oil, ghee
  • rice cakes
  • egg dishes
  • jelly, custard, mousses
  • fruit and vegetables low in fibre (discard the skins)

Foods to Avoid because of risk of contamination:

  • Processed meats: sausages, ham, salami
  • Citrus fruits
  • Nuts and seeds
  • Berries and dried fruit
  • Asian take away food



Fill in your prescriptions for the antibiotics at your chemist and follow the instructions in this protocol. If you have any known drug allergies please inform us prior to commencing any of these antibiotics and alternatives will be prescribed.


Note you cannot drink alcohol at any time when taking these antibiotics as it will interact with the antibiotics and can have severe side effects.


C.diff Infection

  • Vancomycin 500mg twice daily for 10 days
  • Flagyl 400mg three times daily for 10 days

All other Indications

  • Rifaximin 550mg twice daily for 10 days
  • Flagyl 400mg three times daily or Vancomycin 250mg twice daily  for 10 days
  • Nystatin one capsule three times daily for 10 days

Take your antibiotics for 10 days prior to your first FMT and stop antibiotics 24 hrs prior to your first FMT.


Commencing FMT

Our practice is to administer the very first faecal transplant via a colonoscopy. This only needs to be done once. All the remaining transplants will be self administered by rectal enema.


The reason we believe colonoscopy is so important when commencing remicrobialisation is that it allows us to seed the very top of the colon with the new microbiota. This is a critical area to repopulate with good bacteria. It is a long way up the colon, being almost one metre away from the anus and it is where the distal small bowel called the terminal ileum joins the end of the large bowel called the caecum and where the appendix sits.


These three areas, the caecum, the appendix and the terminal ileum are believed to be very important reservoirs or storage houses of good gut bacteria that can be called upon to reconstitute the gut microbiota after an injury such as antibiotics.


The enema FMTs are very effective at implanting a new microbiota but they cannot reach this far up the colon. Therefore, there is concern that enema only FMT may not implant the good bacteria up this far and may miss the ileum, appendix and the caecum. For this reason, we encourage everybody commencing an FMT program to kick off the process of microbiota replacement with the first FMT being performed via a colonoscope.


This will ensure the entire colonic and ileal regions are seeded with the new microbiota. This is the strong recommendation and practice of Prof Tom Borody of CDD, who invented FMT and has achieved the most consistent results to date. We adopt the same opinion. Following your colonoscopy and first FMT all further FMTs will be via enema.


Your diet now changes to a high fibre paleo type diet once you commence FMTs. This is because we now need to nurture the new good gut bacteria and they need fibre.


Bowel Preparation For Colonoscopic FMT

You will need to purchase three sachets of PICOSOLAX - available from pharmacies without prescription or from our clinic. Remember your last dose of antibiotics is to be taken the night before your bowel preparation begins.


Day Before Colonoscopy and First FMT -On Waking in the Morning...

Do Not Eat any Solid Foods


Drink Clear Fluids Only - Clear soups, broths, clear fruit juice, res, coffee, boon, soft drinks


Bowel Wash Out as Follows:

  • 3pm - Dissolve the first sachet of Picosolax in a glass of water or clear juice and drink. Follow with at least 4 glasses of other clear fluids over the next 2 hours.
  • 4pm - Dissolve the second sachet of Picoprep in a glass of water or clear juice and drink. Follow with at least 4 glasses of other clear fluids over the next 2 hours.
  • 5pm - Dissolve the third sachet of Picoprep in a glass of water or clear juice and drink. Follow with at least 4 glasses of other clear fluids over the next 2 hours

You may drink clear fluids between and after sachets up until midnight


Picosolax cleanses the bowel and promotes diarrhoea. Be prepared to visit the toilet regularly throughout the day.

Fast From Midnight Onwards...

In the morning...

on rising, take 2 GASTROSTOP tablets provided for you with a small sip of water. These tablets are only to be taken on the first morning of the infusion and are to assist you retaining the FMT. No other food or drink is allowed until after your colonoscopy and FMT.