Graduate Studies, UNL

 

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

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First Advisor

Kristi Montooth

Degree Name

Doctor of Philosophy (Ph.D.)

Committee Members

Amanda Ramer-Tait, Clay Cressler, Ian Keesey, Jessica Hite

Department

Biological Sciences

Date of this Version

5-5-2026

Document Type

Dissertation

Citation

A dissertation presented to the faculty of the Graduate College at the University of Nebraska in partial fulfillment of requirements for the degree Doctor of Philosophy

Major: Biological Sciences

Under the supervision of Professor Kristi Montooth

Lincoln, Nebraska, May 2026

Comments

Copyright 2026, Nitin Bansal. Used by permission

Abstract

Host-associated microbiomes play central roles in host physiology, development, and susceptibility to disease, yet their composition and stability vary widely across genetic, environmental, and ecological contexts. Understanding the factors that shape microbiome structure remains a key challenge in host–microbe biology. This thesis examines how host genetic background and environmental perturbations independently influence gut microbiome composition in Drosophila, and uses mechanistic modeling to explore how microbial dynamics can affect pathogen invasion outcomes.

In Chapter 1, I investigate how mito-nuclear genetic variation influences gut microbiome structure across developmental stages and generations. Using 16S rRNA sequencing, I show that microbiome composition differs between genotypes and life stages, with genotype-specific patterns of microbial stability and divergence emerging over time. In Chapter 2, I examine how dietary ethanol exposure reshapes the gut microbiome across Drosophila species that vary in their ecological specialization. Because Drosophila species differ in their natural association with fermented substrates, ethanol serves as a biologically relevant environmental stressor for examining microbiome responses across species that occupy specialist and generalist ecological niches. This chapter characterizes shifts in microbiome structure and different bacterial taxa under ethanol exposure. In Chapter 3, I develop a mathematical model of host–microbiome–pathogen dynamics to investigate how microbial acquisition and competition influence pathogen invasion. Focusing on dominant Drosophila gut bacteria, the model provides mechanistic insight into how differences in microbial dynamics can generate variation in infection outcomes. Together, these chapters provide complementary empirical and theoretical perspectives on the drivers of microbiome variation and highlight the value of integrating ecological context with mechanistic modeling to understand host–microbe systems.

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