Corals and algae are the most common benthic competitor on coral reefs and the benthic community is shaped by the interaction between these two groups. Bacteria play an important role in the outcome of the competition between corals and algae. Understanding the role competition and the environment has on the structure of these bacterial communities is important to the field of coral reef ecology. In this thesis, I present a statistical method to understand individual bacterial species' roles within normal coral or algal holobionts. I was able to partition the bacterial community into species of bacteria that were stably or sporadically associated with their host and independently characterized these subgroups. Stable bacteria, together, had a lower relative abundance with the communities but had a high species diversity while sporadic bacteria were abundant but comprised of fewer species. The partitioning of coral and algal holobionts allows for a detailed assessment of bacterial species with different distribution patterns for a given holobiont. Together, the method and analyses presented in this thesis provide a foundation for understanding the complexity of holobiont membership.