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Evolutionary dynamics of the human gut microbiome

Author(s)
Zhao, Shijie
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Massachusetts Institute of Technology. Department of Biology.
Advisor
Eric J. Alm.
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MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission. http://dspace.mit.edu/handle/1721.1/7582
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Abstract
The composite members of the human gut microbiome encounter a myriad of selective pressures from the host environment and other microbial members in the ecosystem. Understanding the evolutionary dynamics of microbial species in the gut microbiome requires sequencing information that differentiates strains and even single cells. In this thesis, I present efforts that investigate the evolution of bacterial strains in their complex natural environments. In the first project, I discover that a commensal species, Bacteroides fragilis, undergoes within-person adaptive evolution in the absence of antibiotics. Combining culture-based whole genome sequencing with metagenomes, I uncover genes important to B. fragilis survival in the human gut microbiome and describe evolutionary dynamics within individuals and across populations. In the second project, I developed a strain-tracking method that predicts personal microbiomes. Using this method to track closely-related strains, I discover signals of adaptive evolution for Bacteroidetes strains, potentially over decades of colonization in adult twins. In the final project, this strain-tracking method is applied to advance the analysis of microbial transmission within social networks of Fiji islanders. These projects demonstrate the power of genome-resolved and strain-resolved methods in revealing insights of evolutionary dynamics of the gut microbiome. Future studies are expected to further investigate other taxonomical groups in depth and technical breakthroughs are needed to improve the throughput of evolutionary studies of complex systems like the gut microbiome.
Description
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2019
 
Cataloged from PDF version of thesis.
 
Includes bibliographical references (pages 156-168).
 
Date issued
2019
URI
https://hdl.handle.net/1721.1/122423
Department
Massachusetts Institute of Technology. Department of Biology
Publisher
Massachusetts Institute of Technology
Keywords
Biology.

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