Reef-building corals form massive calcium carbonate structures that are visible from space and support invaluable reef goods and services. These corals are metaorganisms whose functionality comes from the holobiont integration of the cnidarian host, its primary dinoflagellate endosymbionts (family Symbiodinaceae), and a multitude of bacteria, archaea, viruses, and fungi that are surface, tissue, and skeletal dwelling symbionts. The study of this symbiotic system as a fascinating functional puzzle has intensified with the rapid decline in coral cover and growing threat of reef extinction due to climate change factors, such as increasing seawater temperatures and ocean acidification. In particular, the high frequency of mass bleaching events, where thermal stress causes dysbiosis and loss or expulsion the Symbiodinaceae and mass coral mortality, has sharpened our focus on these threatened organisms. Technological advances have allowed a rapid expansion of coral and symbiont sequence data for studies of coral response to stress, but bioinformatic challenges remain in analyzing and interpreting this wealth of metaorganism data.