Mining the microbiome for markers of microbiota-gut brain communication and mental health
type: CreativeWork
description: There has been a growing acknowledgement of the involvement of the gut microbiome - the collection of microbes that reside in our gut - in regulating our mood and behaviour. This phenomenon is referred to as the microbiota-gut-brain axis. While our techniques to measure the presence and abundance of these microbes has been steadily improving, there are many factors that prevent us from understanding what aspects of the gut microbiome specifically influence the microbiota-gut-brain axis. In this thesis, we set out to identify and investigate aspects of the microbiome that are informative to gut-brain communication. We do this by investigating the state of the gut microbiome in both health and disease, as well as after supplementing or perturbing it. While all of the work presented here is based on real data from real experiments, the thesis has a strong bioinformatics focus, that means that while the physiological background and interpretation are important, my role in these projects has been to bioinformatically and statistically zoom in on the features of the microbiome that are the most informative to our questions. As such, all results will be discussed from a primarily bioinformatics point of view. Two main aspects of the gut microbiome came out as the most promising features to measure, namely functional capacity and volatility. Traditionally, the microbiome is thought of as a collection of microbes and most analysis is done on the taxonomical level. However, we find that by investigating microbial function - as defined by the genes that are found or associated in the detected microbes - rather than taxonomy, we are able to perform more sensitive analysis and that our results are more easily interpretable. Second, microbiome studies are typically conducted using a single sample per subject. We find that the degree of change in the microbial ecosystem, called volatility, is an important feature of the microbiome and that is linked to severity of stress response.…
abstract: There has been a growing acknowledgement of the involvement of the gut microbiome - the collection of microbes that reside in our gut - in regulating our mood and behaviour. This phenomenon is referred to as the microbiota-gut-brain axis. While our techniques to measure the presence and abundance of these microbes has been steadily improving, there are many factors that prevent us from understanding what aspects of the gut microbiome specifically influence the microbiota-gut-brain axis. In this thesis, we set out to identify and investigate aspects of the microbiome that are informative to gut-brain communication. We do this by investigating the state of the gut microbiome in both health and disease, as well as after supplementing or perturbing it. While all of the work presented here is based on real data from real experiments, the thesis has a strong bioinformatics focus, that means that while the physiological background and interpretation are important, my role in these projects has been to bioinformatically and statistically zoom in on the features of the microbiome that are the most informative to our questions. As such, all results will be discussed from a primarily bioinformatics point of view. Two main aspects of the gut microbiome came out as the most promising features to measure, namely functional capacity and volatility. Traditionally, the microbiome is thought of as a collection of microbes and most analysis is done on the taxonomical level. However, we find that by investigating microbial function - as defined by the genes that are found or associated in the detected microbes - rather than taxonomy, we are able to perform more sensitive analysis and that our results are more easily interpretable. Second, microbiome studies are typically conducted using a single sample per subject. We find that the degree of change in the microbial ecosystem, called volatility, is an important feature of the microbiome and that is linked to severity of stress response.…
author: Bastiaanssen, Thomaz F. S.
language: en
keywords: Microbiome, Gut-brain-axis, Bioinformatics, Stress, Depression, Aging
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
date published: 2021-03-29
date modified: 2026-07-24T01:46:20Z
provider: University College Cork
publisher: Networked Digital Library of Theses and Dissertations
type: WebPage
source organization: University College Cork

PropertyValue
property ID: Handle
value: https://hdl.handle.net/10468/11880