There are 100 trillion micro-organisms in the intestinal tract, with the majority of those found in the large intestine. The 100 trillion cells are composed of over 5000 different species of bacteria, fungus, mold, yeast, parasites, etc. Together, all of these micro-organisms create what has been called the densest ecosystem on the planet. Although I'm familiar with the medical diagnosis of bacterial overgrowth, I believe that it is a misdiagnosis founded on a major misunderstanding of this digestive ecosystem. There may be imbalances within certain species of the digestive tract, but overgrowth would be hard to achieve without many factors being altered. One thing that could do this is the use of antibiotics or chemotherapy. If you did have some type of bacterial overgrowth, it would have to be medically induced through medications, so I wouldn't look to the medical for a solution.
A more natural approach would be addressing the dysbiosis and detoxification. I recommend the McCombs Plan as a good place to start.