Research is indicating that the food we eat affects what bacteria populates our gut. Diet dictates the diversity and abundance of the beneficial bacteria that is called our gastrointestinal microbiome. In almost all disease states, the microbiome has lost diversity. This is often the case with autoimmune diseases and GI disorders.
Interestingly enough, research has indicated that obesity has a microbial component that alters the caloric extraction from the food we eat. If you have more Bacteroidetes, you tend to be leaner. High Firmicutes:Bacteroidetes ratios have been know to increase the caloric extraction from food, resulting in an individual who tends to be more obese.