Anyone who is sick or has disease will have a skewed ratio of GI bacteria. What happens is that the number of good bacteria, primarily lactobacillus and bifidobacterium decrease and the number of other bacteria increase. I didn't call them bad bacteria, they are actually normal bacteria but when their concentration ratio increases, problems occur. Eating fiber or inulin containing products provides fuel for the good bacteria and allows them to flourish provided they have room to expand. As our villi become clogged, the surface area for bacterial growth decreases. Eating animal protein, primarily phenylalanine containing products, seems to increase the problems of surface area competition in the small intestine. My recommendation is to only eat animal protein one or twice a week depending on activity level. Nutrient absorption decreases and a leaky gut is the result. When a leaky gut occurs, the bacteria that are normally contained in the GI tract move to other areas of the body and become pathogenic. Bilophila, prevotella, and different bacteria of the streptococcus genus can all translocate to other areas and become pathogens. A lot can be written on this.