Research in Focus: Complex Polymicrobial Biofilms
As part of #BiofilmWeek, we’re highlighting interesting and exciting biofilm research being undertaken across our NBIC partner research institutions by early career researchers, PhD students and our Interdisciplinary Research Fellows.
We interviewed Dr Shaun Robertson, NBIC Interdisciplinary Research Fellow (IRF) from the Biodiscovery Institute at the University of Nottingham. Shaun tells us all about his research which focuses on the development of polymicrobial biofilm models and understanding the interplay between microbes within these biofilms.
What is the title of your current research project or your primary area of biofilm research?
My primary area of research focuses on the understanding of the complex interactions between multiple clinically relevant microbial species, understanding how these microbes interact with each other, and by extension the host cells. This will allow us greater insight in how to potentially prevent and treat these complex polymicrobial biofilms. This will range in the clinical context to wounds, cystic fibrosis and Osteomyelitis.
Are there any collaborators on the project?
For the core research, this is a collaboration between the Nottingham NBIC IRF’s, this includes Dr Manuel Romero and Dr Fadi Soukarieh. For the model development and industrial Proof of Concept projects, our internal University of Nottingham collaborators include, Professor Felicity Rose and Dr Luisa Martinez-Pomares. Externally, a number of the projects have been funded either wholly by industrial funders, or through the NBIC Proof of Concept projects such as that with Io-Cyte or also the NBIC seed funding we have received for collaborations between NBIC IRF’s based at different core universities.
‘The Meeting Of Kingdoms’ – Composite of confocal laser scanning microscopy images of a fluorescently stained inter-kingdom poly-microbial biofilm containing major wound pathogens. Image by Dr Manuel Romero and Dr Shaun Robertson, University of Nottingham.
What is the current situation within your sector?
The majority of the research relates to the healthcare environment, but I also have a NBIC Proof of Concept seed funding which relates to agriculture. For healthcare, it’s well established that the biofilm community, as opposed to the planktonic free-living community, is responsible for around 80% of infections. There is a vastly growing appreciation that there are not only a single species in these biofilms, but polymicrobial, (composed of multiple species) and these will have interactions with themselves, they can cross talk with each other using quorum sensing signal molecules, or also through primary and secondary metabolites etc. The market position for this is that aside from the mortality and morbidity, the financially implications are vast. For example, globally, the impact of biofilms has recently been valued at over $5trillion for all sectors. Agriculturally, the whole sector is reliant on microbes. This is termed the rhizosphere, and is vital for healthy sustained agricultural growth. This is a very important area of research that impacts everyone, as we are potentially nearing a food crisis. If we can help feed disadvantaged countries, that also has vast worldwide consequences and improvements in global health.
What current unmet need does your research address?
Much of the research in the past decade has focused on the prevention and treatment of microbial infections, yet that issue still persists, and there is a large clinical unmet need for development of new antimicrobials, adjunctive therapies and also preventative methods, or combinations thereof, that can help tackle what is a growing Antimicrobial Resistance (AMR) crisis. The research is urgently needed to address this. The unmet need in this area is understanding how these microbes interact together and also how they co-operate to resist the measures that we take. There is also good evidence that these polymicrobial communities are more resistant than their single species or planktonic counterparts. My research aimed for impact in the public and private sectors is to understand how this occurs and also how to manipulate these for beneficial outcomes.
What other emerging economic and societal impacts could the project have? and are there challenges you will have to overcome to achieve impact?
If we could understand these interactions and then manipulate them to have beneficial outcomes that will have a vast societal impact by reducing morbidity and mortality. Economically, the reliance on treatments and cost of treatments will be reduced. Many of the associated costs with these treatments is that these are long lasting chronic conditions. For example, with wound biofilms, it is not just a case of antibiotic treatment and then you are cured. Especially in the case of diabetic foot ulcers, these are lifelong conditions that have to be managed and treated and take up a vast amount of healthcare resources and time. If we can manage these infections and better prevent them, treat them better, shorten that chronic period and get the resolution of the healing of wounds, or reducing the lung function decline of cystic fibrosis patients, these have vast impacts that would be revolutionary. The challenges come as soon as you move towards a more complex system, with multiple species rather than one species, and looking at physiologically relevant conditions and introducing oxygenation differences (such as aerobic, microaerophilic and anaerobic conditions). This modelling of the clinical situation increases the complexity in standardising these systems to get repeatable and reproducible results. Additionally, collaborative work becomes more difficult and it takes more time to validate and standardise these methods, and ultimately is slower than just working with mono species and traditional microbiology outcomes.
What other research is taking place in this field?
We’re seeing quite a shift change in the research focus in the field, progressing from the mono and dual species interactions to focusing now on polymicrobial biofilms, this has been a recent change in the last decade. I think this has been aided by the revolutionary and powerful next generation sequencing, allowing us to understand what actually is in these complex communities, because we used to use culture-based methods, so we were biased as to what we could culture. Now we know there is a lot in there that we couldn’t grow, but is actually there, and it may have an impact on these polymicrobial interactions, or the host outcomes, or it may just be there without being an issue. We need to experiment with this to then understand it. This has also helped with being able to sequence the anaerobic bacteria that otherwise we would be very hard pressed to culture, due to traditional microbiology. Using information in the field we can design better representative models to test prevention and treatment strategies.
Have any key milestones been completed or targets achieved?
I have already completed a number of externally funded research projects, and a recent NBIC Proof of Concept project with Io-Cyte. These all have had successful outcomes. I am looking to publish one of the research projects with one of the externally funded projects in the coming months. The collaboration has been very fruitful from both sides. We have been able to independently verify reproducible results between laboratories, across quite geographically diverse areas, which is a good sign of a number of the targets being completed from the industrial collaboration point of view. There have been a number of publications with myself as co-author, and a number of papers from the other Nottingham IRF’s, so we are working towards these targets and KPIs for NBIC. The fact that we have been able to secure funding being NBIC IRF’s, we’re able to manage these pots of money, which is a useful experience. Compared to traditional research fellow positions, that are working on a single grant on a single project, where you wouldn’t be able to leverage those opportunities, we get as NBIC IRFs, so it has been highly beneficial for us. I think those are also key milestones just getting these grants as well.
Have you received any industry investment NBIC funding and how has this supported your work?
An initial industry investment was the first research project that I undertook when I first came to Nottingham. That aided in the development of a simplified polymicrobial colony biofilm model, which has subsequently gone onto branch out into using this model under different conditions. This has then allowed us to secure further additional funding through a Proof of Concept project, which has been successfully completed. Knowledge gained has also been leveraged to apply a high throughput screening method for the FDA library that we have here, using a polymicrobial screening basis. There has also been funding on another Proof of Concept project recently, that has also been part through the knowledge of the interaction of these microbes and utilising that initial development of the polymicrobial colony model. More recently, work has now started on one of the delayed NBIC seed funded projects between the University of Nottingham and the University of Liverpool. This is an agriculture-based programme, which is looking at the microbial association with crop roots and will focus on crop yield enhancement.
I feel that within the NBIC framework at Nottingham and larger wider NBIC network, we have a combination of very highly skilled diverse colleagues. Just between the Nottingham IRFs we have backgrounds such as microbiology, medicinal chemistry, physics and engineering. I think that provides a distinctive advantage when collaborating on these projects. These are not just single field solutions, they need to be a combination of knowledge bases and experimental techniques, working collaboratively together to come with approaches that are not just straight forward. I think we need a lot of adjunctive methods to be able to progress with these issues. It also helps that Nottingham has world class facilities and leaders of research across the university in multiple fields. I think being able to leverage such a phenomenal level of knowledge and skills is invaluable. The industry benefit of the NBIC Proof of Concept projects where we can develop our ideas and research and see what the issues are in specific areas is very beneficial. It’s all very well having the academic knowledge and understanding, but if you do not have the lived experience, or if you are not on the pulse of what the issues are, it can be sometimes easy to miss-match what you are doing, as to what is required. This is where having clinically relevant collaborations are also useful, which is another excellent thing we have at Nottingham, as we have very good links with the Queens Medical Centre, just across the road from us.
Have you been involved in any public engagement or outreach related to your work?
I have been leading the public engagement at NBIC Nottingham since June 2018 when I started. We organise a number of exhibits at a regional level in Nottingham and Nottinghamshire. These have been particularly successful, and we have had a number of good outcomes from those. These were aimed at all age groups and the attendance was phenomenal. There has been a focus on essentially, ‘what are microbes?’ and by extension, ‘what are biofilms?’ and the influence of our everyday life. I have also contributed towards the development of part of the ‘Super Biomaterials to Fight Super Bugs’ exhibit, which was for the Royal Society summer science exhibition in London, where we demonstrated that activity at the week-long event.
Have you got a favourite memory from these activities?
I would say my favourite outreach memory was using the giant microbes to demonstrate to small children, the reason why we brush our teeth, and showing how these microbes stick to our teeth, so when we brush them, we get rid of them! I think the parents were quite appreciative of that fact, because it re-enforces why their children should brush their teeth. “It’s not just because the need to be clean, it’s because these bugs like to stick to our teeth and then other ones join, and then you get really bad, nasty breath, and we can also get cavities and bad teeth!”. I think it is a really good exercise for teaching children about biofilms by just using these giant microbes and sticking them together.
Find out more
If you are interested in learning more about Shaun’s work and would like to connect with him please contact NBIC at firstname.lastname@example.org.
Shaun Robertson, NBIC Interdisciplinary Research Fellow from the University of Nottingham.