Investigating Microbial Recovery and Colonization Dynamics Across Disturbed Host-Associated Microbial Communities

Microbial colonization is a fundamental ecological process that governs the stability, function, and resilience of microbial communities across diverse environments. This thesis investigates how environmental disturbances shape microbial colonization dynamics in two ecologically distinct but methodologically complementary systems: the human gut microbiome and the phyllosphere microbiome of native California oak trees. In Chapter 1, I explore microbial succession in the human gut by constructing in vitro bacterial communities from stool samples collected from healthy subjects before and after antibiotic exposure. Using these defined synthetic communities that mimic pre- and post-antibiotic microbiota, I introduce novel strains under controlled conditions and assess colonization outcomes using 16S rRNA gene sequencing. These experiments reveal that community composition and competitive interactions are key determinants of colonization success. Colonization patterns vary significantly depending on community context, with several bacterial families exhibiting consistent enrichment or exclusion across trials. These findings provide new insights into the ecological processes that govern microbial community assembly in the gut and suggest strategies for manipulating colonization outcomes in therapeutic settings. In Chapter 2, I turn to the phyllosphere microbiome—those on the surface of the leaves specifically—to study how rainfall and pathogen presence affect microbial diversity and succession in a natural setting. I conduct a longitudinal study of phyllosphere communities on Quercus agrifolia (coast live oak) on Jasper Ridge at Stanford University, comparing trees located near healthy versus Phytophthora ramorum (agent of sudden oak death)-infected bay laurels. Using 16S rRNA sequencing across seasonal rainfall events, I find that rainfall acts as a major disturbance, influencing microbial diversity and selecting for different colonizers. Notably, trees in infected clusters have more bacterial families with greater reduction in relative abundance during rainy periods as compared to the reduction of families in healthy clusters. Patterns of colonization also differ between healthy and infected tree clusters, suggesting that pathogen presence on nearby bay laurels modulates community responses to environmental stress. Together, these studies advance our understanding of microbial colonization and community assembly following disturbance. By integrating controlled in vitro experimentation with ecological fieldwork, this thesis bridges microbiome science across host environments and scales, offering broader insights into resilience, microbial interactions, and the design of interventions in both human and environmental ecosystems for health and conservation purposes.