"Low-fibre Western Diets Deter 'Good Bacteria'"

So eat your fiber. 

"The stools of the African children contained almost three times as many short-chain fatty acids. SCFAs are generated by bugs associated with diets containing a very high proportion of vegetables and cereals... SCFAs kill harmful gut bacteria such as salmonella and help protect against inflammation. Allergies are often the result of an excessive inflammatory response to otherwise harmless agents."

Not only that, but it appears to be a vital nutrient for the bowel:

"It turns out, butyrate [a short-chain fatty acid] has been around in the mammalian gut for so long that the lining of our large intestine has evolved to use it as its primary source of energy. It does more than just feed the bowel, however. It also has potent anti-inflammatory and anti-cancer effects. So much so, that investigators are using oral butyrate supplements and butyrate enemas to treat inflammatory bowel diseases such as Crohn's and ulcerative colitis. Investigators are also suggesting that inflammatory bowel disorders may be caused or exacerbated by a deficiency of butyrate in the first place.

"Butyrate, and other short-chain fatty acids produced by gut bacteria**, has a remarkable effect on intestinal permeability. In tissue culture and live rats, short-chain fatty acids cause a large and rapid decrease in intestinal permeability. Butyrate, or dietary fiber, prevents the loss of intestinal premeability in rat models of ulcerative colitis. This shows that short-chain fatty acids, including butyrate, play an important role in the maintenance of gut barrier integrity. Impaired gut barrier integrity is associated with many diseases, including fatty liver, heart failure and autoimmune diseases..."

Given that the decline in eating fiber was matched by the rise in eating wheat flour, it sounds like a 1-2 punch to the intestinal tract.  Although my own experience was that even eating fiber doesn't do the trick if you're also eating wheat.