Clostridium difficile bacteria live harmlessly in many people's guts alongside hundreds of other species. But some antibiotics can kill off C difficile's competitors, allowing the bugs to multiply and produce masses of toxins.
This can lead to serious diarrhoea and may be fatal.
In the new study, a team of scientists from US and Israel treated 20 people with chronic C difficile infections using frozen faecal capsules.
The capsules were made using faecal material from four carefully screened healthy volunteers.
Each patient was given 15 capsules on two consecutive days.
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After another course of treatment, only two patients had further worrying episodes of diarrhoea.
Scientists have already carried out successful faecal transplants, a therapy that generally involves administering fresh excrement through a tube or directly to the colon.
But researchers argued that this is uncomfortable, impractical and can carry risks for patients.
"The use of capsules simplifies the procedure immensely, potentially making it accessible to a greater population," said Dr Ilan Youngster from Boston Children's Hospital, who was involved in the study.
The study was published in the Journal of the American Medical Association.