This week Science magazine published an article which sheds some light on how the intestine maintains a healthy relationship with microbial flora. I need to talk to a friend in the sciences to better understand the article's content (look for that next week:) However, the article's introductory paragraph aligns with the basic rationale behind the SCD.
Introductory paragraph from the August 29, 2006 Science article:
The human gut is home to a vast consortium of symbiotic bacteria. Members of this complex microflora metabolize dietary substances, such as plant polysaccharides, that are otherwise indigestible by their human hosts (1). Indigenous gut microbes thus make essential contributions to human nutrient metabolism and, in return, inhabit a protected, nutrient-rich environment. Maintaining the mutually beneficial nature of this relationship requires strict sequestration of resident bacteria in the intestinal lumen, as microbial incursions across epithelia can elicit inflammation and sepsis. [bold added]
source: Symbiotic Bacteria Direct Expression of an Intestinal Bactericidal Lectin. Science 25 August 2006: Vol. 313. no. 5790, pp. 1126 - 1130
From the "Science Behind the Diet":
The Specific Carbohydrate Diet is predicated on the understanding that Ulcerative Colitis, Crohn's Disease, Irritable Bowel Syndrome, and gluten therapy resistant Celiac are the consequence of an overgrowth and imbalance of intestinal microbial flora. [bold added]
Of course, the trick is the method in keeping the balance. Other related journal excerpts regarding intestinal flora and IBD may be found here, by numbers (2) and (3): Friendly Bacteria Dramatically Improved A Debilitating Bowel Condition