Genomic exploration of bacterial habitat adaptation

Master's Thesis


In this study we adopted a cross-habitat, comparative genomic approach to identify genetic markers of habitat adaptation in bacterial populations from human gut, marine and soil environments. Although humans depend heavily on microbial activity in these ecosystems, these environments are very different from a microorganism?s perspective. We hypothesized that genetic markers characteristic of one of these three environments would be indicative of the strongest drivers of selection in these environments. Many of the discriminating genetic markers for a given environment mapped well onto environmental characteristics of that environment. For example, bacteria isolated from the human gut environment tended to have the least functional diversity and lacked pathways for amino acid biosynthesis and DNA repair. In contrast, soil and marine bacterial genomes had relatively high functional diversity and possessed abundant pathways for energy production, stress response, and response to a variable environment.


Attribute NameValues
  • etd-04152013-173109

Author Dan Liu
Advisor Stuart E. Jones
Contributor Scott Emrich, Committee Member
Contributor Michael Pfrender, Committee Member
Contributor Stuart E. Jones, Committee Member
Degree Level Master's Thesis
Degree Discipline Biological Sciences
Degree Name Master of Science
Defense Date
  • 2013-04-02

Submission Date 2013-04-15
  • United States of America

  • bacteria

  • adaptation

  • genomics

  • University of Notre Dame

  • English

Record Visibility Public
Content License
  • All rights reserved

Departments and Units

Digital Object Identifier


This DOI is the best way to cite this master's thesis.


Please Note: You may encounter a delay before a download begins. Large or infrequently accessed files can take several minutes to retrieve from our archival storage system.