The human gut microbiome is a dynamic and complex community of microorganismscolonising the gastrointestinal track that is recognised to play an important role in human health. Prevalent in the gut microbiome are plasmids, which are extrachromosomal mobile genetic elements that replicate and disseminate independently of host cellular processes. Plasmids encode antimicrobial resistance and virulence factors, which provide advantageous traits to their microbial hosts. Characterising the spatial and structural organisation of plasmids within microbial communities is essential for understanding the ecology and evolution of natural communities. However, there are currently no techniques to specifically label whole plasmids for visualisation, with current techniques relying on the labelling ofsingle plasmid genes. This project aims to develop an innovative and scalable technology, plasmid fluorescence in situ hybridisation (PlasmidFISH), as a single-cell approach to visualise and comprehensively characterise novel plasmid-host relationships, spatial organisation, and temporal dynamics in the human gut microbiome. The technique has been successfully demonstrated on an Escherichia coli isolate and is now being optimised on faecal samples to visualise whole plasmids in the human gut microbiome for the first time. The ability to track the movement of clinically relevant plasmids through the human gut microbiome will help advance the study of public health concerns such as antimicrobial resistance.