The rumen and gastrointestinal tract of cattle are populated by a dense and diverse microbial population. The complex microbial ecosystems play an important role in ruminant nutrition. We have long known that ruminal bacteria, protozoa, and fungi convert feedstuffs to volatile fatty acids and microbial crude protein which are utilized by the cow. Increasing evidence has accumulated that the microbial population is intimately involved with gut health, gut integrity, and the proper function of the immune system. The microbial population of the gut produces acids and other compounds that contribute to the development of conditions such as sub acute ruminal (or cecal) acidosis (SARA) which can lead to leaky gut syndrome, laminitis, and systemic inflammation in the host animal. If we can modulate the gastrointestinal microbial population, we can affect gut integrity and alter the immune system in ways that reduce inflammation, enhance gut health, improve nutrient uptake, and reduce carriage of opportunistic foodborne pathogenic bacteria. Some of the most effective methods to modify the microbiome involves the use of direct-fed microbials (DFM), which includes probiotics and prebiotics. Prebiotics are nutrients that are not utilized by the host animal but are degraded by microbes, whereas probiotics are live or dead microbial products or the end products of their fermentation. Feeding DFM products can have profound effects on the gut microbial population, because they create changes in specific microbial ecological factors that affect survival of microbes and the end products of the gastrointestinal fermentation. Shifts in the VFA proportions can profoundly affect the growth of cattle, milk production, gut health, and energy available for gestation, lactation, or growth. By shifting the composition of the microbial population, we can change the microbial impacts felt by the animal and thus. Including pre- and probiotic products in dairy rations can improve gut health and integrity, immune responses, animal health, and food safety of dairy cattle.