Beyond the Biofilm: Illuminating the Hidden World of Microbes

From Science Fiction to the Science of Infection

My interest in science has been present for as long as I can remember, though identifying a single point of origin is difficult. According to my parents, it was likely encouraged by visits to the Science Museum in London during my childhood, experiences that fostered a sense of curiosity and wonder about how the world works. My own enjoyment of science fiction also played a role, as its combination of imagination and scientific possibility has always resonated with me.

My introduction to microbiology came later. Initially, I intended to pursue medicine, believing it to be the primary route for studying infectious diseases. However, I soon discovered that microbiology provided a more direct and investigative approach to understanding pathogenic organisms and their mechanisms of how they cause disease. This realisation was pivotal, as it revealed a pathway that combined my fascination with fundamental biological processes and my interest in addressing real-world challenges related to infection and disease.

Bringing Biofilms into Focus

I work across the Schools of Pharmacy and Life Sciences at the University of Nottingham, investigating how modern imaging techniques can be combined to better understand biofilm formation and its dynamic interactions with the surrounding environment. My research focuses on developing and refining imaging methodologies, such as confocal and atomic force microscopy combined with optical nanosensors, to map chemical and physical changes, including pH, within biofilms over time. This approach aims to reveal new spatial information and relationships between bacterial behaviour, environmental shifts, and the resulting properties and architecture of the biofilm as a whole.

While I’m still in the method development phase of the project (having just started my second year!), the aim is to create imaging tools that can be applied to real biofilm systems to answer biological questions, such as how local environmental changes influence bacterial behaviour and biofilm structure. This kind of information is directly relevant to antimicrobial resistance, as biofilms are key in disease virulence and persistence, contributing to antimicrobial tolerance and resistance. Understanding their structure–function relationships at this level could inform more targeted and effective intervention strategies.

Overall, my work aims to develop visualisation strategies to study how bacterial biofilms form, adapt, and survive within their environments. By using nanosensor-based imaging to map environmental changes within biofilms, such as shifts in pH, I hope to uncover how these microenvironments support bacterial resilience. In the long term, this knowledge could help design more effective strategies to disrupt harmful biofilms and monitor how well antimicrobial treatments target them.
A 3D Breakthrough

One of the most exciting milestones so far has been achieving true correlation of multiple datasets in three dimensions capturing bacterial distribution, environmental information, surface topography, and the material characteristics of a biofilm, such as how sticky or stiff it is.

While that might not sound like a dramatic breakthrough, it’s a crucial step for my project. It demonstrates the proof of concept of bring together structural, environmental, and mechanical data into a single 3D picture, which opens up a lot of new possibilities for understanding how biofilms develop and interact with their surroundings.

For me, it was a really satisfying point in the project, seeing the method I’d been developing for months finally work as intended and start generating meaningful data. It gave me confidence that the approach was possible and that the time spent refining each step was worthwhile. More importantly, it confirmed that the system can now serve as a foundation for exploring the next stages of the project.

Extending Support Beyond Undergraduate Study

Having worked in higher education and now returning as a postgraduate student, I’ve seen how much progress universities have made in improving diversity and inclusion. Over the past decade, the range and visibility of student support services have expanded greatly, which is a real positive step forward, and something I highly applaud these services for developing these pathways for said support.

One area that still needs attention, though, is the gap between the support available to undergraduate and postgraduate students. From my experience both as staff signposting students to services and now as a researcher personally accessing them, this seems to be a sector-wide challenge rather than a university-specific one. Strengthening postgraduate support in line with undergraduate support would address this gap and help ensure postgraduate researchers have access to the same level of support and inclusion as their undergraduate peers.

Lessons from the Lab and Beyond

I wouldn’t say I’ve had a single mentor as such, but I’m very much the product of the time, encouragement, and patience of many people who’ve guided me throughout my career. My family instilled a strong work ethic and a belief in putting genuine effort into everything you do. At school, my science teachers really opened the world of science to me. They entertained my endless “why?” questions, and made science feel like a living, breathing subject rather than just a set of facts.

Early in my early career, working in an NHS pathology lab alongside biomedical scientists taught me the value of diligence, reliability, and attention to detail and it’s where I really expanded and develop my wet lab technical skills. In higher education and academia, I’ve been fortunate to work alongside people whose enthusiasm for discovery and passion for their fields are genuinely infectious. That love of science is something I’ve tried to carry forward and share with others.

In many ways, I’m a product of all those interactions and lessons a reflection of the time, patience, and generosity of the people who’ve supported me throughout my career. Each of them, in their own way, helped shape how I think about science, how I work with others, and how I try to contribute to teams.

Building Knowledge and Community

So far, the National Biofilms Innovation Centre (NBIC) has provided me with multiple learning and outreach opportunities which I have gladly accepted! Recently I was given a great introduction to genomics run by Dr Joe Parker at the University of Southampton. This course served as a fantastic starting point for learning about the modern-day application of these technologies and how we can utilize them to study complicated polymicrobial biofilms.

Additionally I have taken part in some outreach run by NBIC during the Festival of Science and Curiosity in Nottingham, where I had the opportunity to chat with the younger members of the public about science and microbiology, something I highly suggest to other PhD students to get involved with.

Exploring What Comes Next

By the end of my PhD, I hope to have published several papers some through collaborations and others from smaller grant funded projects. These experiences will (hopefully!) help me develop the skills needed to lead my own research in the future and exploring the interface between pathogens and their hosts, an area of microbiology that I find very interesting. I’m particularly interested in how emerging nanotechnologies can be used to probe these complex boundaries in new ways, revealing the finely tuned mechanisms which bacteria use to cause disease.

The field is increasingly moving toward more correlative and multidisciplinary techniques to generate large spatial datasets. Over the last decade, the tools, computing power, and hardware needed to achieve this have developed rapidly transforming what once felt like “sci-fi” into everyday science.

So rather than one specific breakthrough, what excites me most are those moments when something that once seemed impossible suddenly becomes routine and feeling that excitement of, “Wait, we can do that now?!” Those moments capture exactly why I love being part of microbiology!

Find out more

If you are interested in learning more about Jordan’s work and would like to connect, please contact NBIC at nbic@biofilms.ac.uk

Jordan Kirby, second year PhD student at the University of Nottingham.