In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biology in the School of Biological Sciences D. Joshua Parris will defend his dissertation Microbiome Community Change in the Guts Of Marine Fish: Feeding and Life Stage Transition as Significant Organizing Factors.

Thesis Advisor:
Dr. Frank Stewart
School of Biological Sciences
Georgia Institute of Technology

Committee members:
Dr. Mark Hay
School of Biological Sciences
Georgia Institute of Technology

Dr. Tom DiChristina
School of Biological Sciences
Georgia Institute of Technology

Dr. Julia Kubanek
School of Biological Sciences
Georgia Institute of Technology

Dr. Kostas T. Konstantinidis
School of Civil and Environmental Engineering
Georgia Institute of Technology

Summary
All animals harbor microbial communities (microbiomes) that play vital roles in host health, development, behavior, and evolution. Determining the processes that regulate microbiome diversity and function is therefore a central question in biology. Numerous investigations have sought to quantify the influence of factors such as diet, host genotype, and environment on gut microbiome assembly, taxonomic composition, and function (Spor et al. 2011, Koenig et al. 2011, Myles et al. 2013). However, these studies have been mostly limited to a handful of model or commercially important host systems. We remain naïve in our understanding of how the importance of different microbiome assembly processes might vary among diverse hosts. This is especially true for the most phylogenetically and ecologically diverse of the vertebrate groups, teleost fishes. In this dissertation, I first describe compositional changes in the gut microbiome associated with the transition from a pelagic larval stage to reef settlement in damselfish (Pomacentridae) and cardinalfish (Apogonidae). Results identify a key transition in microbiome structure across host life stage, suggesting changes in the functional contribution of microbiomes over development in two ecologically dominant reef fish families. Next, I use the clownfish Premnas biaculeatus to test how diversity, predicted gene content, and gene transcription of the microbiome vary over a diurnal period following a feeding event. Results confirm feeding as a major restructuring force in intestinal microbiomes over a short timeframe (hours). Finally, I describe ongoing work to characterize the phylogenetic novelty and functional capability of a fish-associated Endozoicomonas bacterium. While this genus has been identified as a symbiont of marine invertebrates, its role in the guts of fish remains unknown.  Together, these studies advance our understanding of the diversity and potential function of the fish microbiome, setting the stage for studies to identify the microbiome’s effect on fish health and ecology.