The latest feature article in Cell Host & Microbe supports the rationale behind the specific carbohydrate diet (SCD).

The science section of Breaking the Vicious Cycle (BTVC) describes intestinal flora becoming unbalanced due to reasons such as overuse of antibiotics, malnutrition, and poor diet.  BTVC proposes that this imbalance eventually results in intestinal inflammation.

Similarly, the authors of "Cell Host & Microbe" article write:

"We propose that a disruption of such balances [of gastrointestinal bacteria] contributes to human disorders such as inflammatory bowel disease and colon cancer."

Later in the article, the authors propose that genetics predispose many people to IBD, but they emphasize that "environmental factors play a significant role in disease." 

The article mentions "antibiotics, enteric infections, diet" as factors which can disrupt the balance of intestinal flora and lead to inflammation.

The latest cell research is showing that certain types of gut bacteria "communicate" with intestinal cells, regulating the immune response.  For example, intestinal bacteria can influence inflammation--valuable in some cases, but dangerous/painful to us if it becomes chronic as in IBD.

source: "A Pathobiont of the Microbiota Balances Host Colonization and Intestinal Inflammation", Cell Host & Microbe 7, 265–276, April 22, 2010.

related article: Caltech Biologists Link Gut Microbial Equilibrium to Inflammatory Bowel Disease