From genomes to populations : measuring the microbiome at small and large scales
Abstract/Contents
- Abstract
- A comprehensive understanding of the presence, function, and variation of gut mi- crobiomes across populations is important for relating the gut microbiome and hu- man health. However, most efforts in the microbiome field have been grounded in fragmented microbial reference genomes derived from a non-representative sub- set of the world's population. These limitations can constrain associations between genome-level and population-level microbial variation and downstream effects on hu- man health and disease. This dissertation focuses on leveraging cutting-edge metage- nomics approaches to more accurately and comprehensively measure human gut mi- crobes. I present five projects that collectively detail the characterization of the gut microbiome across biological and experimental scales, from building complete mi- crobial genomes to measuring microbiome variation across global cohorts. Chapter 1 provides an introduction to the current state and recent advances in microbiome research. Chapter 2 details molecular and computational pipelines to recover com- plete, contiguous microbial genomes from metagenomes, which represents a significant technical advance. Chapter 3 further describes these protocols in a detailed and ac- cessible manner to enable broader research in this space. Chapter 4 presents the first application of a new synthetic long-read sequencing assay to the problem of metagenomic assembly. Transitioning more broadly to accurate microbial measure- ment on experimental and methodological scales, Chapter 5 compares how sample preservation methods introduce experimental bias and affect microbial concentration quantification. Finally, widening scope to the measurement of microbiome variation across global populations, Chapter 6 presents a study of the gut microbiome of two South African populations and places their microbiome composition in global con- text. Together, these studies advance our ability to measure microbiomes, through building accurate microbial genome representations, thoughtfully considering study design and the importance of measured variables, and providing a concrete framework for conducting community-engaged, large-scale global studies.
Description
| 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 | 2023; ©2023 |
| Publication date | 2023; 2023 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Maghini, Dylan Gabriele |
|---|---|
| Degree supervisor | Bhatt, Ami (Ami Siddharth) |
| Thesis advisor | Bhatt, Ami (Ami Siddharth) |
| Thesis advisor | Good, Benjamin H |
| Thesis advisor | Sherlock, Gavin |
| Thesis advisor | Sidow, Arend |
| Degree committee member | Good, Benjamin H |
| Degree committee member | Sherlock, Gavin |
| Degree committee member | Sidow, Arend |
| Associated with | Stanford University, School of Medicine |
| Associated with | Stanford University, Department of Genetics |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Dylan Maghini. |
|---|---|
| Note | Submitted to the Department of Genetics. |
| Thesis | Thesis Ph.D. Stanford University 2023. |
| Location | https://purl.stanford.edu/jw286dr8020 |
Access conditions
- Copyright
- © 2023 by Dylan Gabriele Maghini
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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