Doctoral Dissertations

Date of Award


Degree Type


Degree Name

Doctor of Philosophy



Major Professor

Sarah L. Lebeis

Committee Members

Gladys Alexandre, Alison Buchan, Chunlei Su


While microbes inhabit a wide array of environments, their ability to live within host tissue and become tolerated as part of a select microbial community is perhaps one of the most impressive feats of microbial resilience and survival. Host microbiome establishment and maintenance requires both host-microbe and microbe-microbe interactions. Among plant hosts, benefits from associated microbiomes are known to include improved growth, development and resistance to abiotic and biotic stresses. Mammalian microbiomes are known to improve host digestion, influence inflammation and even improve immune response to pathogens. While host-associated microbial communities across all domains of life are incredibly diverse, a growing number of studies are finding host-specific taxonomic trends, suggesting microbiome conservation and evolutionary selection. However, we have come to recognize that there is often functional redundancy between taxa. Therefore, investigative focus on microbiome composition potentially neglects pivotal and influential microbial players. Shifting focus to function over form creates the opportunity to tease apart the driving forces of unique microbiome constituents. This allows for identification of strains and genes of interest as well as microbial selections. To that end, here we describe the relationships between hosts and microbiomes as well as between microbes in two vastly different host systems (Figure 1.1). First, we suggest that plant root-associated Streptomyces isolates harboring genes encoding an enzyme and its co-factor are more tolerant of phenolic compounds generated by roots. Next, we address the capability of these Streptomyces isolates to employ their metabolic repertoires to influence the composition of the root microbiome. Finally, we define a previously under-described role for the gut microbiome in malaria immunology and suggest that gut microbial composition can modulate the severity of malarial disease. Together, these findings demonstrate the broad implications of microbiome composition across diverse hosts and environments, revealing unexplored opportunities for therapeutic interventions aimed at improving plant and human health.

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