Microbiomes of Long-Tailed Macaques in Southeast Asia: Prokaryotic and Eukaryotic Interactions

The interior and exterior margins of vertebrate bodies are blurred by the microbes occupying these spaces. Microbial assemblages associated with a host are thus built and shaped by a multitude of sources which originate from both the host and the environment. Host functions and external environment exhibit ‘inside-out’ control over residential and introduced bacteria, leading to the fluctuation or depletion of a host-associated bacterial community composition. Bacteria exhibit ‘outside-in’ behavior in turn, presenting products and functions of their own immune system to the host. In addition, host behaviors such as foraging, eating, and physical contact with other hosts provide nearly constant influxes of microbes which act to replenish populations and introduce competition to existing communities. Eukaryotic microbes, such as protozoans and helminths, add to the already incredibly dynamic mixture of organisms associated with a mammalian host, inducing control over cohabiting microbes as well as the host.

This dissertation aims to analyze host-associated microbiome dynamics on varying scales and increase our understanding of the underlying interactions by expanding our scope to include eukaryotes. First, I examine site-specific bacterial communities of long-tailed macaques in Singapore, concentrating on the oral and gut microbiomes and how they vary through geographical space. Revealed in this work is evidence showing that, though oral microbes have greater diversity than gut microbiomes, they show greater similarity across geographic space, which reflects their role as a barrier between hosts and the environment in which they live. Next, I expand this work to Bali, Indonesia, and examine the differences of gut bacterial microbiomes across landscapes through host diet. I find macaque diets vary with location, and that this variation is associated with changes in the gut bacterial community. I then show how macaque consumption of plants with medicinal properties is tied to parasite presence by incorporating a medicinal database as a framework to evaluate diet-parasite interactions. Finally, I find variation of gut parasites of macaques to be driven by the protozoan Blastocystis and extend this finding to analyze the prokaryotic microbiome, the diversity and composition of which shifts in the presence of Blastocystis. Collectively, this work shows that aims to understand mechanisms driving host-microbiome relationships fall short without considering eukaryotic context.