A study from the American Journal of Gastroenterology from 2012 shows evidence that germ-free mice are protected against obesity. It is only when gut microbes from conventionally raised animals are transferred to these mice that there are dramatic increases in body fat and insulin resistance.
First, let me define conventionally raised animals. Conventionally raised beef for example, will usually be given antibiotics during its life to keep it healthy. Frequently, it will also be given hormones to increase its size quickly. When it is time to finish the beef the cow will be transferred to a feedlot, a small, crowded area that doesn't allow the cow to move much. Here it will be fed a specially formulated feed until it is ready to be butchered. The feedlots are dirty, unsanitary, and unpleasant for both the animals and those that work with them. This is in comparison to grass fed beef. Grass fed beef, as defined by the AGA, (American Grass-fed Association) defines grass-fed animals as those that have eaten nothing but grass and forage from weaning to harvest, have not been raised in confinement, and have never been fed antibiotics or growth hormones. In addition, all AGA-Certified Producers are American family farms and their livestock is born and raised in the U.S.
The study mentioned above, also showed that the composition of gut microbiota differs in lean and obese humans and animals and can change rapidly in response to dietary factors. The gut microbiota may also influence the development of conditions causing low-level inflammation, such as obesity and type 2 diabetes, through systemic exposure to bacterial lipopolysaccharide derived from the intestinal microbes. Lipopolysaccharides are large molecules consisting of a lipid and a polysaccharide. They are found in the outer membrane of gram negative bacteria and cause strong immune responses in animals. Lipopolysaccharides send signals to certain cells that play a role in the immune system response. This data suggests that modification of the gut microbiota may be a relevant therapeutic treatment for obesity and other metabolic disorders.
Although this study does prove that modification of the gut microbiome can help treat obesity and possibly diabetes type 2, there remains to be many unanswered questions requiring further research. The most optimal composition of the gut microbiota is still poorly understood. Attempting to modify the microbiome can be detrimental and should be pursued with caution.
For more information on human microbiomes check out this link to Genome Magazine