A food, a prebiotic as it's called, increases the numbers of correct bowel bacteria and not the incorrect flora such as yeast, clostridia, e. coli and such. Inulin is not used by human digestive enzymes so it reaches the large intestine to be used by the correct bacteria, which feed on it, proliferate, and control the "bad guys". Inulin can be used most significantly by bifidobacteria, and somewhat by lactobacilli, both of which are beneficial organisms. By using this non-drug approach you do not wipe out most of the good or neutral bowel bacteria in addition to the 'bad' ones as Antibiotics do.
Although "native" inulin cannot be used by undesirable, putrefactive bacteria such as C. perfringens, C. difficile, or E. coli to any great extent, some people do experience some bowel disturbance because it contains about 6% Sugar that yeast can feed on, and 2% FOS that many undesireable bacteria can use. A much more specific prebiotic, FOS- and sugar-free inulin, appeals to even fewer bad bacteria.
Sugar- and FOS-free inulin is diabetic- and candida-safe, and it's preferred by those with bowel candida, irritable bowel syndrome, colitis and Crohn's disease, all of which are usually acompanied by incorrect bowel bacteria, or "gut dysbiosis".
The Science is on my website. This is perhaps the best online resource and it's the ONLY source of the excellent study, Inulin: A Comprehensive Scientific Review.