One of the most promising areas looks to be looking at our gut bacteria, called the microbiome, and the use of probiotics that may help positively change our gut bacteria.  The studies in labs and on animals are starting to look promising on a variety of strains.  For example, we can put bacteria from an obese mouse into the gut of a thin mouse and make them obese and vice versa we can put gut bacteria from a lean mouse and keep them lean.  So, in theory, this may be possible one day for humans but it is just too early to say.  

A number of trials have been done already and shown very mixed results, either no weight loss, some minor weight gain or at best a minor benefit like only 1kg or 2 lbs.  And this is for a significant financial cost of between $30-50 a month. And some probiotics can potentially cause side effects like gut cramping and constipation   

So at this point, it is clear that the gut microbiota plays an important role in body weight and fat but that trying to fix that with probiotics we have at the moment does nearly nothing for a significant cost. This is an area of large-scale research so I say this so you know to keep an eye out.