If the essential gut flora (good bacteria) in the gut is damaged or weakened and not functioning as they should, then the ‘walls of the city’ are not protected very well and open to invasion by anything that comes along including trouble from the opportunistic flora. In inflammatory bowel disease different pathogens are found in the mucosa, even inside the gut cells, which means that the protective bacterial band has been broken and allowed the pathogens to reach the sacred gut wall.
Without a well-functioning gut, the gut wall not only becomes unprotected but also malnourished. Normal gut flora provides a major source of energy and nourishment for the cells which are lining the digestive tract. The beneficial bacteria living on the gut epithelium digest the food which comes along, converting it into nourishing substances for the gut lining. When the gut flora is compromised, the lack of nourishment it would produce adds to the damage of the digestive wall structure which would further impair the ability to digest and absorb nutrients. The absorptive surface of intestines has a wonderful structure of finger-like protrusions, called villi, and deep crypts between them. The epithelial cells called entrocytes, which coat the villi are the very cells which complete the digestive process and absorb the nutrients from food. Since they work very hard, these cells need to remain young. They are constantly born in the depts of the crypts. Then they slowly travel to the top to the villi, digesting and absorbing and getting more mature on the way to the top of the villi where they shed off. This way the epithelium of the intestines gets constantly renewed to ensure its ability to do the work well. When the essential bacteria (the house keepers) living in the intestinal epithelium are removed, this process of cell renewal gets completely out of order - upsets the maturation process of enterocytes, less and less of them are born health, the whole structure of gut epithelium changes, starting a process of pathology or disease developing. The villi degenerate and become unable to digest and absorb food properly, leading to malabsorption, nutritional deficiencies and food intolerances and often these cells turn cancerous.