A molecular investigation of signalling and microbial niche dynamics in host, environment, and food ecosystems
Loading...
Files
Date
2025
Authors
Woods, David F.
Journal Title
Journal ISSN
Volume Title
Publisher
University College Cork
Published Version
Abstract
Food, environmental and host ecosystems are inhabited by dynamic communities of life and the spatial and temporal heterogeneity of micro and macro ecology in these niches remains poorly understood. The challenges posed in understanding and sustaining traditional food processes, arresting the continued decline in biodiversity, and addressing the increase in chronic disease in an ageing population, are such that the profiling, conservation and sustainability of our microbial niches has never been more relevant. Microbial niches encompass biotic and abiotic components. Complex interactions occur within these niches between the microbial milieux. Compositional structural changes are often driven by unknown dynamic signalling. Failure to characterise these niches and the associated signals, can result in the loss of valuable and novel beneficial applications pertinent to the areas of food sustainability, green pharmaceuticals, and medicinal health. To address this, the integration of molecular technologies, culturomics, and bioinformatic technologies provides a powerful toolkit for investigating complex microbial niches. Three microbial niches were explored by molecular techniques to profile the signalling and niche microbial structural dynamics. The key microbial niches profiled by molecular investigation were, 1) a Food process for more sustainable and reproducible Wiltshire curing, 2) an Environmental niche to access novel bioactives from the untapped marine ecosystem and 3) the profiling of a Host to investigate the drivers and signals of microbial pathogenesis in the respiratory disease of Cystic Fibrosis. Profiling, defining and monitoring these microbial niches has many advantageous outcomes for improved processing, novel applications, and health. Through molecular techniques and culturomics, the bacterial content of an active Wiltshire cure was quantified, the core microbiome was defined for the first time, and key beneficial bacteria identified with potential food safety and preservation functions such as quorum quenching and catalase activity. In the marine niche, molecular and bioinformatic screening revealed novel biocatalysts, specifically transaminases and esterases. Both enzymes represent valuable resources for greener pharmaceutical production of Active Pharmaceutical Ingredients (APIs). Moreover, signalling molecules were used to communicate bacterial growth in culture, unlocking previously inaccessible marine microorganisms. Providing further resources to unlock the untapped resource of the marine environment. The pathophysiology and disease progression of the Cystic Fibrosis (CF) lung niche was also explored. The analysis of this niche revealed that bile exposure was associated with microbial compositional change. Further, molecular and signalling investigation demonstrated that the hormone has a role in the immunomodulation of human CF respiratory cells, as well as influencing the metabolic activity, and the transition from acute to chronic infection of the respiratory pathogen, Pseudomonas aeruginosa. This thesis demonstrates the applicability of using molecular tools to investigate microbial niche dynamics and the beneficial practical outcome in food, environmental, and host ecosystems.
Description
Controlled Access
Keywords
Microbiome , Wiltshire curing , Next Generation Sequencing , Molecular gastronomy , Green chemistry , Biocatalysis , Biodiscovery , Cystic Fibrosis , Chronic infection , Pathogen , Inflammation , Pseudomonas aeruginosa
Citation
Woods, D. F. 2025. A molecular investigation of signalling and microbial niche dynamics in host, environment, and food ecosystems. PhD Thesis, University College Cork.