Comparative analysis of the gut microbiome in lemurs (Order: Primates)

Abstract

<p>Host fitness is impacted by trillions of bacteria in the gastrointestinal tract (GIT) that facilitate development of the intestines and brain, digest fiber, and defend against pathogenic invasion. Gut microbes are closely tied to host development and, by extension, the components of life history. Yet, because microbes are capable of lateral gene transfer across vast phylogenetic distances, scientists have struggled to determine whether the taxonomic (microbiota) or genetic (microbiome) composition of a microbial community plays a greater role in its symbiosis with the host. The overarching theme of this dissertation is to explore the interplay between the phylogeny and phenotype of both host and its microbiome. By using 16S rRNA gene amplicon sequencing, metagenomic sequencing, and metabolomics to compare gut microbial communities associated with captive hosts, we are able to identify which microbial community features are correlated with specific host factors. First we compared gut colonization in infants across three lemur species with different diets and gut morphologies. Next we used metagenomic sequencing and nuclear magnetic resonance (NMR) spectroscopy to assess the suite of metabolic pathways and products associated with each host species. Both studies suggest that fiber is a critical dietary component associated with key features of microbial colonization in healthy infants. We next compared bacterial lineages shared between lemurs and bamboo specialists to assess which specific classes of microbial membership are impacted by host phylogeny versus diet. Finally, we compared secondary colonization trajectories to assess the impact of Cryptosporidium, an intestinal pathogen that seasonally infects captive sifakas at the Duke Lemur Center. We find that, while diet predictably shapes community structure and function during colonization, disease incurs age-related impacts on each individual’s microbiome uniquely.</p>