Defining and modelling the microbiome in chronic obstructive pulmonary disease
Creators: name: Short, Bryn
Publisher: name: Zenodo
Year: 2024

description: Chronic obstructive pulmonary disease (COPD), a chronic and degenerative lung disease, is the third leading cause of death worldwide, claiming the lives of approximately 6.1 million people annually. Progression of COPD is reliant on several factors from host genetics to lifestyle choices. One factor that drives disease progression, which has received increasing amounts of attention in the past decade, is the lung microbiome. However, what is still unclear is the mechanisms by which this occurs. COPD patients are chronically colonised by bacterial pathogens and experience frequent respiratory infections as a result of compromised clearance mechanisms. All the above evidence points towards the presence of biofilms within the COPD lung.Firstly, using bioinformatic approaches the literature surrounding the area of the microbiome in COPD was analysed to identify past, current and potential future trends as well as any gaps in current knowledge of the microbiome in COPD. Further work aimed to clarify the role of the microbiome in COPD and address current limitations that were identified in the bioinformatic-based literature search. While identifying a bias towards certain bacteria, no other clear trends were observed. In contrast to cystic fibrosis, which showed evidence of functional analysis, the COPD microbiome literature showed no evidence of this and therefore revealed what is lacking in our understanding of the COPD microbiome and therefore identified a potential future trend.Secondly, using in silico approaches, a meta-analysis of the lung microbiome in health and COPD was performed. Throughout the COPD microbiome literature, there are some conflicting findings surrounding aspects such as bacterial diversity and the presence or absence of certain organisms. Therefore, the following analyses aimed to address this.This was achieved through the secondary analysis of microbiome sequencing data that had been deposited into online repositories. This analysis identified that study-specific experimental design features were behind the conflicting findings in the literature, indicating that less study-to-study variation in sample collection and processing methods would improve our ability to properly synthesise results in meta-analyses such as this one.No significant differences were observed in the diversity of the healthy and COPD lung microbiomes and key members of the COPD microbiome were identified as bacteriaassociated with the oropharynx such as Streptococcus, Haemophilus, Moraxella, Prevotella, Staphylococcus and Porphyromonas. Next, to address some of the limitations in the literature surrounding the functionality of the microbiome, enriched metabolic pathways of the COPD microbiome were identified. This analysis revealed an enrichment of bacterial virulence associated pathways, indicating the mechanisms by which the microbiome can drive inflammation in COPD. Next, a multi-species biofilm model, containing bacteria and fungi, was developed and characterised by assessing its antimicrobial susceptibilities and immunogenicity. This biofilm model contained bacteria identified within the meta-analysis in the previous chapter. Characterisation of this model revealed Candida albicans as a key member of thebiofilm which promoted bacterial growth by acting as a substrate for the bacteria to bind. These interactions lead to multi-species biofilms being highly tolerant to antimicrobial therapies that are commonly used in COPD therapy. Even in combination, antifungals and antibiotics were not sufficient to kill or remove the biofilm. Supernatants from these biofilms also displayed an ability to elicit an immune response from epithelial cells. This was then increased following antimicrobial treatment. These findings point towards, oropharyngeal bacteria interacting with fungi in the respiratory tract, promotingantimicrobial tolerance and driving inflammation.Lastly, the effects of bacteria on C. albicans at a transcriptional level were investigated with the intentions of identifying potential mechanisms behind the increased antimicrobial tolerance and immunogenicity observed in the previous chapter. Bacteria were found to increase fungal virulence within a biofilm environment and therefore other potential mechanisms by which the COPD microbiome drives lung inflammation were identified. Future studies should continue to address current limitations in the literature, in particular the functionality of the COPD microbiome and developing ways in which it can be accurately studied in vitro.