The human gastrointestinal (GI) tract is home to an immense number of microbe species that are constantly interacting with each other and with the host’s cells. This ecosystem, composed of bacteria, fungi, archaea, viruses, and the host’s cells, has been found to play an important role in maintaining the overall health of the host. Many of these microbes are responsible for producing metabolites that directly benefit the host by supplementing nutrition needs, improving the integrity of certain cellular structure, serving as cell signalers, and acting as an additional countermeasure against pathogens. In this chapter, we go over the important microbial groups that are present in the GI tract and have been known to impact human health. We will go over their functions, their metabolic processes, and the specific health-related outcomes that have been associated with the presence of these groups. Further, we go over some of the factors, conditions, and pressures that influence the diversity and quantity of specific microbial populations.