How to Make Microbiota Capsules

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fecal transplant capsules

“just think playdough”


While some FMT practitioners use capsules, others strongly advise against it. The reason for this is that your upper intestine is meant to be almost sterile, so top-down FMT may cause/aggravate SIBO (small intestine bacterial overgrowth). You’re particularly at risk if you have low stomach acid and/or motility problems. So please don’t take risks. Always discuss with your doctor.


double up the capsules, placing small into large


  • 2 pairs silicon gloves
  • 3 plastic containers
  • 2 sets of gelatin capsules, small & large (entero-coated capsules if possible or roll in beeswax)
  • plastic sheet / towel
  • 1 fresh sample of Fecal Microbiota



  • Open the capsules and put them into separate containers. 
  • Put on gloves.
  • Roll sample like playdough to a shape that will slip easily into the smaller capsules.
  • Fill the smaller capsules taking care to protect them from moisture. Some people use a syringe for this part.
  • Change gloves.
  • Place the smaller capsules into the larger capsules.
  • Consume capsules on an empty stomach to minimise damage from stomach acids.
  • Take with lots of water to push the FMT as far down the small intestine as possible.
  • Consume as soon as possible to preserve the diversity of microbiota. 
  • Capsules can be frozen
  • Using entero-coated capsules or rolling in beeswax will prolong the trip down the gut, ensuring delivery of microbiota lower down


  • It’s important to protect the capsules from moisture so that they don’t melt too soon. The double capsule helps prevent leakage. 
  • Gelatin capsules are widely available. Entero-coated (gastric acid resistant) capsules can be purchased here and here. These are optional, however can help to protect the microbiota from stomach acid and delay its release until further down the small intestine. Some have made their own entero-coated capsules by dipping standard gelatin capsules in beeswax. 
  • You can buy a capsule-maker here and here (mixed reports) however most find it easier to make them by hand. 

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