The MicroBiomica contribution
At UCD, Dr Guerrino Macori and the MicroBiomica Lab will lead research combining long-read metagenomics, microbial genomics, bioinformatics and predictive modelling to investigate antimicrobial resistance reservoirs and transmission across One Health environments.
A major component of our work will be the generation and analysis of long-read metagenomic data from farm, food-production, environmental and wildlife sources. Using Oxford Nanopore sequencing alongside genomic and microbiological approaches, we will investigate microbial communities, antimicrobial resistance genes, mobile genetic elements and their genomic context.
An important research direction will be the study of microbial dark matter: microorganisms and genomic sequences that remain poorly represented in current reference databases. Rather than restricting AMR surveillance to already characterised organisms, we will investigate whether these uncharacterised components of microbial communities represent overlooked reservoirs of resistance genes and mobile genetic elements.
The project will also integrate metagenomic information with bacterial whole-genome sequencing, antimicrobial resistance phenotypes and environmental metadata. Computational approaches, including taxonomy-independent analysis, unsupervised learning and machine learning, will be developed and applied to identify patterns associated with the emergence, persistence and transmission of AMR.
Ultimately, this integrated information will contribute to predictive models and risk mapping aimed at identifying environments and conditions in which antimicrobial resistance may be more likely to emerge or spread.