Research indicates that FOS enhances the growth of Bifidobacteria, Lactobacillus acidophilus and a few other Lactobacilli species. Harmful bacteria, such as Citrobacter, E. coli, Salmonella and Clostridium can not utilize FOS. Therefore, supplementing a diet with FOS complements and expands the benefits of direct-fed microbial supplementation and selectively feeds the beneficial bacteria to tip the microbial balance in favor of good health. Microbiologists find that L. acidophilus and the Bifidobacterium reduce the growth of pathogenic bacteria, promote nutrient absorption and may enhance the immune system, among other desirable traits. Young animals and those on milk-based diets have high populations of Bifidobacterium. Unfortunately, the levels of these health-promoting bacteria decline when animals are weaned and as they age.

A study with Beagle dogs found that digestive tract numbers of Lactobacilli and Bifidobacterium numbers increased significantly after two weeks of FOS supplementation.
The benefits of FOS supplementation were evaluated with sixteen German Shepherd dogs with small intestinal bacteria overgrowth and a deficiency of immunoglobulin-A (associated with the digestive tract). The dogs receiving FOS had lower small intestine levels of the pathogenic bacteria. Similar studies with livestock and humans also indicate a healthier microbial balance in the digestive tract of those receiving FOS