Making FMT

One of the biggest challenges of DIY FMT is that you have to prepare it yourself — and for many people, the idea of handling human stool can feel confronting or downright unpleasant. That said, the major advantage is cost: DIY FMT is vastly more affordable compared to the thousands of dollars it can cost to undergo the procedure in a clinic. There are several methods for preparing and administering DIY FMT, but I personally used the fleet enema method demonstrated by a woman in the U.S. who successfully treated her daughter’s C. difficile infection at home. Youtube instructions: FMT via fleet enema

An alternative method: DIY FMT enemas

This is an excellent resource for all things FMT, although in my opinion, Maximilian sets unrealistically high standards when it comes to selecting FMT donors: FMT resources

Collection

The donor will need to collect their stool sample in a clean, sealable container. If the FMT can’t be prepared immediately, the sample should be placed in the fridge as soon as possible. For transport, keep the sample in a cooler (like an esky) at around 4°C to slow microbial die-off. The sooner you prepare the FMT, the better — ideally within 8 hours of collection — to preserve the highest microbial viability. Once prepared, the FMT can either be administered fresh or mixed with a cryoprotectant and frozen for future use.

This recommendation is from the article: A Guide for Ex Vivo Handling and Storage of Stool Samples Intended for Fecal Microbiota Transplantation “If, for logistical reasons, waiting time would be greater than 24 hours, then it will be crucial not to expose samples to temperatures above 20 °C. In that respect, refrigeration at 4 °C for short-term storage and shipment can be a preferred solution.”

Items needed to make FMT fleet enemas

You’ll need to purchase a small smoothie blender. Ours cost ~$35. Something like this: Smoothie blender
Fleet enema 133ml bottles. You’ll most likely have to order these online as I’ve never seen them in an actual pharmacy. They seem to be ~$5-$8 each. You may be able to shop around and get them cheaper: Photo of Fleet enema
Saline solution. You can make your own 0.9% saline solution (with iodine free salt) or just purchase it. It can’t be the saline solution people use for their contact lenses as that contains antibacterial agents. This Baxter sodium chloride 0.9% is what we purchased before we started making our own saline solution: Baxter saline solution photo
If you are going to freeze the FMT for later use you will need to add 10% USP glycerine to the saline solution as it is a cryoprotectant and will reduce microbial die-off when the FMT is later thawed (just google USP food grade glycerine). Food Grade Glycerine photo. Maltodextrin powder may be a more effective cryoprotectant than glycerine, potentially reducing microbial die-off upon thawing. Using maltodextrin instead of glycerine could therefore be advisable, although I have not personally tried it.

Plastic jug
Spoon
Metal strainer that fits over the plastic jug

Making FMT

Refer to the Youtube instructions: FMT via fleet enema

If you plan to administer the FMT immediately, simply add saline solution to the stool in the blender. However, if you intend to freeze the FMT, you’ll need to add a cryoprotectant such as food-grade glycerine. I typically keep two separate bottles on hand: one with just saline, and another with 10% glycerine mixed into the saline (for example, for a 1-litre bottle, I combine 900 ml of saline with 100 ml of glycerine).

You want enough saline or saline-glycerine solution to create a slurry that is runny but still somewhat thick. I don’t measure this precisely since stool volume can vary significantly. In my experience, the runnier the slurry, the harder it is to hold the FMT in comfortably—you really feel the urge to use the toilet.

Some people avoid using a blender due to concerns about oxygen exposure killing anaerobic microbes. While some die-off may occur during blending, in our experience, enough microbial diversity remains. The blending is brief and intermittent—just enough to create a slurry, not continuous. If you’re very concerned about oxygenation, you might want to follow the alternative methods shown in the YouTube videos I previously shared.

After making the slurry, I strain out the solids using a fine strainer into a plastic jug, then fill the fleet enema bottles with the liquid. This is important because if you don’t strain the solids, the enema bottle’s tip will get clogged.

*Note: Be sure to empty the original liquid from the fleet enema bottle, rinse the empty bottle and remove the stopper from the lid to allow the FMT slurry to flow freely during administering.

If you’re freezing your FMT preparations, I recommend labelling each Fleet enema bottle with the date it was made as well as an expiration date three months later. While I’ve heard of people successfully using frozen FMTs up to a year old, it’s safest to use them within three months and discard any remaining after that time.

To thaw frozen FMTs, you can either place them in the fridge to thaw slowly or use a quicker method by submerging them in a warm water bath (ensuring that the water is not warmer than body temperature). I typically set a timer for 15 minutes, then replace the water and set the timer for another 15 minutes. After this process, the FMT should be fully thawed and ready for use.

Administering the fleet enema

Alex usually inserted the FMT for me (because I was initially nervous about spilling it), but I later learnt to administer it myself. Instructions: Administration of enema

Administer the FMT in an empty bowel:I recommend doing FMT enema on a day when you don’t need to leave the house afterward, or alternatively, once you’ve returned home from work or other activities. Holding the FMT in for several hours can be challenging, and you may need to rush to the toilet unexpectedly—so it’s best to be in a comfortable, private setting during this time. My advice is to try and hold the enema in for as long as possible, preferably many hours to increase the likelihood of engraftment. I typically found it most difficult to hold it in initially and had to overcome the urge to go to the toilet. After a period of uncomfortableness I usually found this urge subsided and I could easily hold the enema in for many hours.

Making FMT Pills

Here’s a 30 minute video on how to make FMT capsules using capsule machines: Do-it-yourself FMT Capsules

Here is a different method: DIY FMT capsules. Maltodextrin antifreeze method.

In my experience experimenting with FMT capsules, I initially followed the standard advice to use a saline solution with 10% glycerine. However, I found that the saline solution caused the capsules to dissolve. The only method that consistently worked for me was creating the FMT slurry using 100% food-grade glycerine. While this isn’t ideal, I’ve prepared FMT capsules this way for a number of people, all of whom experienced improvements or full resolution of their depressive symptoms suggesting that using 100% food-grade glycerine doesn't significantly negatively impact microbial diversity in the freezing and thawing process.

Unlike one of the commonly shared video tutorials, I didn’t mix the stool and glycerine by hand in a bowl. Instead, I placed both ingredients directly into a blender and gave it a short blitz—just enough to form a slurry, but not so much that it overly oxygenated the sample. Glycerine is more viscous than saline, so you need much less of it to create a suitable slurry.

Once blended, I strained the mixture through a metal sieve into a plastic jug, just as I do when preparing enemas. I then transferred the liquid into an empty Fleet enema bottle, which works well for filling capsules due to its squeezable design.

You can make a lot of capsules from a single stool. When I was using FMT capsules to treat post-viral fatigue, I would consume a fresh batch of about 20 capsules immediately, then freeze the rest. The frozen capsules are taken straight from the freezer. Fresh capsules likely pack a stronger microbial punch, but frozen ones still seem effective.

You don’t need to completely fill the capsules; in fact, I advise against it. Overfilling can cause a mess when pressing the capsule machine together. I recommend storing finished capsules in a plastic container in the freezer with a silica sachet to absorb moisture, and consuming them within a few weeks. If the capsules start to discolour or soften, it’s best to discard them.

At first, I was double-encapsulating the FMT, but I’ve since moved to triple encapsulation. I use size 0 and 00 enteric-coated capsules (to survive stomach acid) and place them inside a coloured size 000 vegetable or gelatin capsule—mainly for aesthetic reasons, so you can’t see the contents. My hope is that triple encapsulation reduces the risk of early breakdown in the stomach.

Some people suggest that enteric coating isn’t necessary, and that it’s fine for the capsules to open in the stomach. Personally, I think that’s risky. Stomach acid would likely destroy a large portion of the microbes. Conversations I’ve had with microbiome researchers involved in FMT trials confirm that enteric-coated capsules are the recommended approach.

Consuming FMT pills

Several studies and protocols on oral FMT have specified fasting before consumption to maximise microbial survival. Taking FMT capsules on an empty stomach reduces stomach acid levels, speeds up gastric emptying, allowing the capsules to pass into the intestines more quickly and minimises the risk of premature capsule breakdown before reaching the small intestine.

The recommendation is to consume FMT pills on an empty stomach, typically:

Firs thing in the morning, or
At least 2-3 hours after a meal, and
Avoid eating for at least 1 hour afterward.
(I personally found it easiest to consume them 2-3 hours after dinner and before bed)

Items needed to FMT pills

(these websites are obviously in Australia but these items should be easily obtained)

Blender, FMT bottle, strainer etc, which you will already have to make FMT enemas
Food grade glycerine
Enteric coated capsules size 0 and size 00 (delayed release capsules that won’t break down in the stomach). 200 Size 00 Enteric Coated Delayed Release Capsules - Clear
Size 0 and size 00 capsule filler: (the capsule filler machines are excellent and make it really easy to make a lot of pills quickly) CAPSULE MACHINE Capsule Filler Size '00'
I prepare the FMT slurry using 100% glycerine and transfer it into a Fleet enema bottle, as the nozzle makes it very easy to fill capsules (though a syringe would also work). I first fill size 0 enteric-coated capsules with the slurry, then place those inside size 00 enteric-coated capsules, and finally encase them in coloured size 000 gelatin capsules. Size 000 White Gelatin capsules
Size 000 capsule filler machine: CAPSULE MACHINE Capsule Filler Size '000'
To slow down microbial death, I would fill up the size 0 capsules with the FMT slurry then put the fleet enema bottle into the refrigerator in between filling up the capsule machines.

Alternative method for making FMT pills: DIY FMT capsules. Maltodextrin antifreeze method.