Development of methods for the microbiome analysis of formalin fixed paraffin embedded tissue specimens
type: CreativeWork
description: For Synthetic Biology to reach its potential, it necessitates foundational knowledge of the organisms that can be engineered. The remarkable influence our microbiome has on our health status has made it a focus of attention for engineering possibilities aiming at its modulation. As the field of the human microbiome expands, it necessitates access to high-quality nucleic acid samples which are truly representative of the community of bacteria under study. Formalin-fixed, paraffin-embedded (FFPE) samples represent the most comprehensive collections of patient materials in hospital pathology archives. However, for this sample to become reliably accessible for microbiome studies, the effects of FFPE processing on bacteria must be considered. Any sample processing method should be based upon specific study aims, target organisms and sample types. It is only through a holistic understanding of FFPE-induced changes to the bacterial cellular structure and its DNA content, that a reliable method can be developed It is hypothesised here that with a sample-prep workflow considering the effects of FFPE on bacterial cells, their DNA content and the overall contamination introduced, a reliable and reproducible analysis of the microbiome of FFPE samples could be achieved. As such, the overall aim of this thesis was to characterise FFPE induced changes to the bacterial cell walls/membranes and their DNA content, and with this information, to propose strategies for purifying and repairing DNA suitable for microbiome analysis, while also characterising the common contaminants found in samples processed in this manner. To achieve this, an appropriate FFPE bacterial study model was first developed. With this in place, a thorough characterisation of the state of bacterial FFPE DNA was performed and strategies to reduce this damage assessed. Finally, to develop an appropriate method for bacterial DNA extraction from FFPE samples (unavailable at the time of writing), the state of the bact…
abstract: For Synthetic Biology to reach its potential, it necessitates foundational knowledge of the organisms that can be engineered. The remarkable influence our microbiome has on our health status has made it a focus of attention for engineering possibilities aiming at its modulation. As the field of the human microbiome expands, it necessitates access to high-quality nucleic acid samples which are truly representative of the community of bacteria under study. Formalin-fixed, paraffin-embedded (FFPE) samples represent the most comprehensive collections of patient materials in hospital pathology archives. However, for this sample to become reliably accessible for microbiome studies, the effects of FFPE processing on bacteria must be considered. Any sample processing method should be based upon specific study aims, target organisms and sample types. It is only through a holistic understanding of FFPE-induced changes to the bacterial cellular structure and its DNA content, that a reliable method can be developed It is hypothesised here that with a sample-prep workflow considering the effects of FFPE on bacterial cells, their DNA content and the overall contamination introduced, a reliable and reproducible analysis of the microbiome of FFPE samples could be achieved. As such, the overall aim of this thesis was to characterise FFPE induced changes to the bacterial cell walls/membranes and their DNA content, and with this information, to propose strategies for purifying and repairing DNA suitable for microbiome analysis, while also characterising the common contaminants found in samples processed in this manner. To achieve this, an appropriate FFPE bacterial study model was first developed. With this in place, a thorough characterisation of the state of bacterial FFPE DNA was performed and strategies to reduce this damage assessed. Finally, to develop an appropriate method for bacterial DNA extraction from FFPE samples (unavailable at the time of writing), the state of the bact…
author: Flores, Yensi
language: en
keywords: Microbiome, FFPE, Standards, Methods
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
date published: 2019-04-30
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/10468/10095