Thesis Format
Monograph
Degree
Master of Science
Program
Anatomy and Cell Biology
Supervisor
Dumeaux, Vanessa
Abstract
Host-adapted microbial communities, or microbiomes, consist of commensal, symbiotic, and pathogenic microorganisms localized to specific body sites. The human gut microbiome, encompassing bacteria, viruses, archaea, and small eukaryotes such as fungi, expresses an estimated 3.3 million genes. These cells play integral roles in human digestion, metabolism, and immune function.
This research aims to profile complex microbial communities in human stool samples to understand the potential impact of exercise on gut microbial functionalities. While metatranscriptomics (MT) provides a global view of community gene expression, single-cell RNA (scRNA) profiling identifies transcriptional changes in individual cells, offering insights into phenotypic heterogeneity. Although scRNA profiling of mammalian cells is established, microbial scRNA profiling presents challenges. This work addresses these challenges by testing different permeabilization and rRNA depletion techniques for fragile cells.
Overall, this research emphasizes the importance of functional profiling of the gut microbiome, advancing approaches for refined profiling with potential biomedical, environmental, food sciences, and synthetic biology applications.
Summary for Lay Audience
Many bacteria and other tiny organisms live inside living beings, including humans, forming microbiomes. The human gut microbiome alone contains around 3.3 million genes, playing crucial roles in digestion, metabolism, and immune defense. This research aims to understand the roles these microbes play by studying their gene expression, particularly focusing on how exercise can influence the gut microbiome. We collected stool samples from sedentary individuals before and after an 8-week exercise program to analyze changes in the microbial community's functionality.
My research aims to understand the roles these microbes play by studying their gene expression using two methods: bulk metatranscriptomics (MT) and single-cell RNA profiling (scRNA). To do this effectively, we are refining techniques to make microbial cell walls permeable and to capture small amounts of microbial RNA. My goal is to adapt current MT profiling to study the human gut microbiome and to develop a reliable scRNA assay, called sc-MC (single-cell RNA profiling for complex microbial communities), to study gene activity in individual microbial cells within complex communities. This newly developed sc-MC assay aims to provide insights into the functions of various microbiomes. As our knowledge of microbial communities advances, this assay has potential applications in fields like medicine, the environment, food science, and synthetic biology.
Recommended Citation
Wang, Qianrui (Ray), "Functional Profiling of the Gut Microbiome from Bulk to Single-Cell: A Pilot Study on Exercise-Induced Effects" (2024). Electronic Thesis and Dissertation Repository. 10282.
https://ir.lib.uwo.ca/etd/10282