The human gut microbiome is increasingly recognized as a key player in health and disease, with influence over digestion, immunity, and even neurological conditions. However, studying how this complex microbial community evolves over time remains a major challenge. Existing DNA sequencing technologies, although powerful, often fall short when it comes to capturing large-scale genome structures or delivering results quickly enough for real-time or longitudinal studies.
This project, Plas_OpMap, tackles this gap by advancing an emerging technology known as optical DNA mapping. Unlike conventional sequencing, which fragments DNA into short pieces, optical mapping visualises entire DNA molecules, allowing scientists to observe large-scale structural variations. This approach is particularly useful for understanding microbiome composition and dynamics. But despite its promise, optical mapping is currently limited by slow imaging speeds and the need for lengthy data acquisition, making it impractical for high-throughput applications.
A major innovation proposed in Plas_OpMap is the use of plasmon-enhanced fluorescence to significantly boost the speed and precision of DNA imaging. This involves placing fluorescently labelled DNA on specially engineered plasmonic substrates-surfaces coated with gold nanostructures that amplify the emission of light from fluorescent tags. By enhancing photon output, these substrates reduce the time needed to capture each image, allowing faster data collection without sacrificing resolution.
The project focuses on developing a reliable and scalable plasmonic substrate using wet-chemically synthesized gold nanotriangles. These nanoparticles are deposited uniformly across a glass surface, creating a dense, stable, and optically active layer. Their unique geometry and material properties support strong plasmon resonances that enhance fluorescence signals from DNA molecules positioned nearby. This design avoids the complexity of conventional nanofabrication and can be adapted to existing imaging setups.
Three key objectives guide the project:
1.Develop and optimize plasmonic substrates with high nanoparticle coverage.
2.Validate the enhancement effect on fluorescence imaging of labelled DNA molecules.
3.Demonstrate optical mapping of DNA extracted from human gut microbiota using the new substrate.
By combining nanomaterials, microscopy, molecular biology, and bioinformatics, Plas_OpMap brings together expertise across several scientific domains. The long-term goal is to enable faster, more scalable genomic analysis tools that support real-time monitoring of microbial populations that are critical for personalized medicine, diagnostics, and environmental health.
While the project is focused on gut microbiome research, the underlying platform has broader potential across biomedical fields. Faster optical mapping could improve how we track infections, study disease progression, and even respond to public health challenges. In this way, Plas_OpMap contributes to the EU’s broader goals in health innovation, research infrastructure, and digital health technologies.
