Date of Award

Spring 6-6-2025

Document Type

Thesis (Undergraduate)

Degree Name

<-- Please Select One -->

Department

Environmental Studies

First Advisor

Bala Chaudhary

Second Advisor

Douglas Bolger

Abstract

Understanding how diverse microbial taxa coexist in the human body without competitively excluding one another remains a key challenge in microbiome ecology. One proposed explanation is the colonization-persistence trade-off, where species with high colonization ability are poor persisters, and vice versa. We test for this trade-off across human associated microbial communities among many individuals and in multiple body sites using a large-scale participant-level meta-analysis of longitudinal microbiome datasets curated from the MGnify database. We applied island biogeography-based models to calculate effective colonization and persistence rates for microbial families and genera across 606 individuals over twenty-six studies. Regression of the log-transformed colonization and persistence rates of different taxa revealed a widespread, significantly negative relationship across all body habitats (gut, skin, oral, respiratory, and vaginal), consistent with the predicted trade-off. We also found that this relationship varies with body habitat, disease state, and temporal variability. The oral microbiome was found to have a shallower (less negative) slope between colonization and persistence, indicating that the cost for persistence is lower for species with high colonization ability. Disease states were associated with a stronger trade-off (slope closer to -1) than healthy individuals, except in the vaginal microbiome where disease was associated with a weaker trade off. High temporal variability in community composition was also associated with a weaker trade-off signal. At the family level, colonization and persistence rates were context dependent, with some taxa acting as colonizers in one habitat and persisters in another. Our findings suggest that the colonization-persistence trade-off structures the diversity of human-associated microbial communities.

Download

Share

COinS