From metagenomes to genomes : new tools for complex bacterial communities

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Characterizing the individual genomes of organisms within the human gut microbiome is a critical first step toward understanding this complex community as a whole and its impact on many aspects of human health. Thus far, efforts to characterize the genome sequences of gut microbiome bacteria have been largely based on short read sequencing and reference-based tools. Although these have benefited from advances in short read assembly and binning approaches as well as large-scale sequencing efforts, they face fundamental limitations that necessitate improved methods for metagenomic sequencing and assembly. This dissertation details some of the molecular and informatic challenges facing the field of metagenomic research within the gut microbiome, explores the limits of the existing methodologies, offers novel technological solutions, and applies those solutions to uncover novel biological insights into the gut microbiome. Chapter 2 describes the application of existing short read-based approaches to the gut microbiomes of cancer patients receiving fecal microbial transplant. Chapter 3 describes a new approach using read cloud sequencing to improve metagenomic assembly. Chapter 4 applies this read cloud approach to study insertion sequence mobilization within bacterial strains over the course of a patient's treatment for a hematological malignancy. Finally, chapter 5 describes a second new approach using nanopore long read sequencing to assemble full-length genomes directly from human gut metagenomes. Together, these chapters provide a deeper understanding of the challenges facing metagenomic assembly of the human gut microbiome, two new approaches to solve them, and new biological insights they have revealed.


Type of resource text
Form electronic resource; remote; computer; online resource
Extent 1 online resource.
Place California
Place [Stanford, California]
Publisher [Stanford University]
Copyright date 2019; ©2019
Publication date 2019; 2019
Issuance monographic
Language English


Author Moss, Eli
Degree supervisor Bhatt, Ami (Ami Siddharth)
Thesis advisor Bhatt, Ami (Ami Siddharth)
Thesis advisor Fordyce, Polly
Thesis advisor Sherlock, Gavin
Thesis advisor Snyder, Michael, Ph. D
Degree committee member Fordyce, Polly
Degree committee member Sherlock, Gavin
Degree committee member Snyder, Michael, Ph. D
Associated with Stanford University, Department of Genetics.


Genre Theses
Genre Text

Bibliographic information

Statement of responsibility Eli L. Moss.
Note Submitted to the Department of Genetics.
Thesis Thesis Ph.D. Stanford University 2019.
Location electronic resource

Access conditions

© 2019 by Eli Moss
This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).

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