Reasons for your worsening stomach problems on a paleo/ low-carb/ ancestral/ gaps/ etc. diet

With all these success stories about people feeling better on various diets, I think we forgot the people who sometimes feel worse. Probably because those people give up and don't stick around. I'm known many people who have adopted paleo, primal, ancestral, low-carb, gluten-free, or whatever diet. And instead of feeling better, they have all kinds of problems, particularly stomach problems. 

There are many reasons why this happens, here are a couple I tend to come across:

The Omega-6 GERD Connection

 While I was doing research on variations in gastric acidity, I came across an interesting paper: Diet, reflux and the development of squamous cell carcinoma of the esophagus in Africa. It's interesting that a lot of conventional dietary advice on digestion is based on studies done in Africa that found that African agrarian cultures eating low-fat high-fiber diets had low rates of common Western digestive issues like hemorrhoids and colon cancer.

The Human Colon in Evolution: Part 4, The Secrets of Butyrate

 Another hypothesis is that lack of SCFAs is behind such diseases of civilization. A SCFA called butyrate provides some insight into this. Butyrate is the preferred fuel of the colonic epithelial cells and also plays a major role in the regulation of cell proliferation and differentiation (Wong, de Souza, Kendall, Emam, & D. J. a Jenkins, 2006). Lower than normal levels have been found in patients with several diseases, notably types of colitis and inflammatory bowel disorder. Studies show such diseases can be treated through application of butyrate in the colon.

The Human Colon in Evolution: Part 3, Creepy Crawlies in the Gut

 The fact that humans cannot digest certain fibers and starches in the diet does not mean they are nothing but bulking matter. In the scientific world, more and more research focus has been on the fact that these seemingly indigestible ingredients actually are often digested in the human body, just not by human enzymes. Instead, they are digested by human gut bacteria.

The Human Colon in Evolution: Part 2, Fiber Foolishness

Suggestions that humans may have obtained more calories from SCFA in the past are rooted in estimates of fiber consumption from the Paleolithic. Evidence is rather sparse and limited to coprolites. In the burgeoning field of evolutionary medicine, anthropologists have become very interested in the Paleolithic diet and its relevance for promoting health today. Some of the landmark papers in the field have cited these coprolite studies as evidence for fiber intakes as high as 150 grams as day, well over what any known human culture currently consumes (M. Konner & S Boyd Eaton, 2010).

Paradise Lost?