As well as looking at whether it can help with weight loss, it is also the first study that will look at a number of other factors such as whether healthy gut bacteria can protect them from diabetes, improve bowel habits and can make them feel better.
The study will follow the 14-18-year-olds for six months and uses gut bacteria taken from four men and four women.
The bacteria is removed from the waste and put inside two capsules so that it does not break open until they reach the bowel and have the best impact.
"Finding donors was challenging in that we wanted the healthiest donors possible because they are the are the vectors of the good treatment. We wanted donors that are lean, that were fit, who exercise regularly, have a healthy diet and didn't have any medical problems."
Of those who volunteered to be donors, only 10 per cent fitted the high criteria.
The study will be completed between the end of March and June and the large amount of information will then be analysed.
"Ultimately if this turns out to be effective treatment, we don't want to rely on donors, we want to be able to identify the range of bacteria."
Cutwell said he drew on his background as a paediatrician to carry out a study on obese teens because there were few treatments available for them. Curbing obesity at an early age could also prevent other health problems such as heart and liver disease later in life.