Welcome to the growing archive of ECR blogposts on our OMIG site. Thanks to all contributors.

APRIL BLOGPOST – PGR SYMPOSIUM MARCH 26th

OMIG PGR Prize Symposium 2021

For the first official blogpost on the new website, we thought to revisit our recent PGR Prize Symposium held on Friday 26th March 2021. This was held entirely virtually using the Hopin platform with a range of different 10-minute oral and poster presentations, each designed to be drop-in style series of sessions for our 80 registrants. Across the whole day, a steady audience of roughly 40 people were present, with numbers fluctuating across the sessions dependant on the topic presented. Admittedly, we were a little apprehensive at first, but given the oral microbiology and immunology PGR community across the UK being relatively small in comparison to other societies, we were overjoyed to reach such numbers of attendees.

We had 16 presenters in total from across the UK, based at a range of different dental institutions such as Kings College London and the Universities of Glasgow, Sheffield, Liverpool and Bristol. A notable mention to the Sheffield Hallam University cohort too, proving that OMIG is not only exclusive to the dental school community!

A total of 5 students ranging from first to final year PhD candidates presented their work in poster “flash session” format. Biophysics PhD student Aileen Delaney from the University of Leeds was voted favourite poster entitled “Using Microfluidics, Raman Spectroscopy and Microbubbles to Investigate and Control Oral Biofilms.” This goes to show that OMIG has a multi-disciplinary membership!


Many congratulations to Aileen Delaney of the University of Leeds for winning best poster presentation.

Aileen who is a 2nd year PhD student in the School of Physics and Astronomy at University of Leeds, shared an overview of her research and experience on the day. “I am based in Molecular and Nanoscale Physics group in Leeds where many of us look at biological structures and try to use physics to get a better understanding of how things work. My work involves using Raman spectroscopy to learn more about biofilms, and specifically how the bacteria interact with each other in a 5-species oral biofilm model. As a physicist, it was really nice to hear about other work in the oral microbiology community at the PGR symposium, and to see how it overlaps with some of the work I do. I thought the layout of the conference was really good too, having posters available for people to browse all day was a nice feature and talks were a good length and easy to ask any questions.”

In total we heard 11 oral presentations across the day. These topics ranged from in vitro oral biofilm model systems, virulence factors of oral microbes, antimicrobial testing and the connection between the oral microbiome and systemic diseases. In sponsorship with the Journal of Medical Microbiology (Microbiology Society), we awarded the best oral presentation to final year PhD student Tracy Young of the Oral Sciences Research Group at the University of Glasgow for her talk on “Polymicrobial Oral Biofilms and the Importance of C. albicans as a “Keystone” Component”.


The vast array of topics presented by students at the recent OMIG PGR symposium.

Tracy who is weeks away from her PhD viva (good luck!) had some pleasant words to say about the PGR symposium experience. “I thought it was a really great symposium highlighting the many different aspects of oral microbiology and immunology work being carried out. I believe it helped early career researchers and PhD students to maybe think outside the box of their own research and that can only be a good thing in advancing the field. I thought the day was successful and that the timings were just right in terms of breaks/number of presentations. I did have some pre-presentation nerves in the backstage “area” particularly as I had never used the Hopin platform but everything went smoothly and I’m grateful to OMIG for the opportunity to present my work”.


Many congratulations to Tracy Young of the University of Glasgow for winning best oral presentation. Many thanks to Journal of Medical Microbiology (MicroSoc) for sponsoring the prize!

The stats from the website confirm that we had plenty of engagement on our main stage and attendees asked plenty of exciting questions. We would like to thank everyone for their attendance and hope to see you all in person for the next OMIG symposium!

 
The engagement from the audience on the day.

Blogpost by Jason Brown and Ricarda Streich.

MAY BLOGPOST – ECR discussion with PhD student, William Johnston

I am delighted to announce the first monthly OMIG discussion with the early career researchers from the society. The purpose of these blogposts is to highlight the research of leading ECRs in the field of OMIG. In the first blogpost below, PhD student William Johnston from the University of Glasgow will introduce himself and discuss his work on investigating the host inflammatory and microbiological responses in periodontitis patients following therapy.

Will in his natural habitat of the class II microbiological hood!
  • Who are you and what is your background? where you are from, qualifications, current position etc.

I am a third year PhD student at the University of Glasgow. I am originally from Glasgow although I spent a large portion of my life in the United Arab Emirates where I attended high school. In 2014 I returned to the UK for my undergraduate studies in Biomedical Science at Glasgow Caledonian University. As part of my undergraduate studies, I undertook a 6-month placement in NHS Microbiology laboratories at Dumfries and Galloway Royal Infirmary, where I subsequently worked as an Associate Practitioner for a further 4 months. In 2018 I graduated with a 1st class honours degree and started my current PhD project the same year.

  • What is your current research on? Can you discuss the key findings from your recent publication?

Most recently I have been working on a longitudinal study we performed at Glasgow Dental School, looking at the host and microbial response following non-surgical periodontal therapy. From this study, we primarily wanted to see how the immune response and subgingival plaque microbiome were altered by this mechanical form of treatment. Additionally, we investigated whether any host or microbial marker was associated with residual disease, and whether the baseline microbiota may be used to predict treatment success!

Following treatment, we found widespread alterations in the composition of the subgingival plaque microbiota. This included a reduction in the diversity of the subgingival plaque and reduced abundance of disease associated species! We also performed some association networks and found a residual anaerobic core, with Rothia negatively correlating with some of these genera (figure below)! This is really interesting and something that should be looked into further, as we discuss a few interesting mechanisms that might be driving this association! From an inflammatory perspective we also found a positive association between salivary IL-1β and periodontal disease severity, and consistent reductions in this marker following treatment!

Genus-level association network at day 90. Graph taken from figure 5 of the manuscript.
  • Where there any unusual results from the study? Any challenges etc that you struggled to overcome?

Although we saw a lot of host and microbial changes following treatment, unfortunately we did not find any predictive capacity of the microbiota when we looked at treatment response. Additionally, we found that salivary IL-17A actually increased following treatment which was very surprising. The literature on salivary IL-17A is quite varied and we are currently looking in some of our other longitudinal studies to see if similar alterations are present, and why this is happening!

In terms of challenges, I started my PhD project with no background in clinical dentistry. It was a big learning curve to understand all the different clinical parameters, but I had a lot of help from our team in Glasgow. Learning how to analyse microbiome data was also very challenging (and intimidating!), so I’m very grateful to our statistical team in Glasgow and collaborators in Valencia that guided me through the maze!

  • What was the publication process like? Were SciReps are journal that you would publish in again? Any challenging reviewers comments?

Overall, I had a very good experience with Scientific Reports. The handling Editor kept us updated on the progress of our manuscript and found reviewers quickly. All in our manuscript took 5 months from submission to acceptance, although this did include 2 review rounds and some additional analysis. It was quite daunting at first reading all of the reviewer’s comments, but they definitely improved the quality of our paper! The reviewer’s suggested some extra analysis which took some time, but it was a good suggestion and addressed some aspects we had initially overlooked, so I have no complaints!

  • What are the next steps with regard to the study? Are any further papers in the pipeline…

Although we showed microbial and immunological alterations after treatment, we only included a single timepoint (day 90). It would be really interesting to study both earlier and later timepoints, which would allow us to see how the biofilm and immune response recover and how long these shifts are maintained. I am currently working on another clinical study we ran at Glasgow and hopefully we can address some of these questions!

  • Any tips to new research Masters or PhD students on getting their work published?

My best advice would be to start with what message you want to convey, and build the paper around this. One of the most difficult aspects I found was selecting which figures go in the main manuscript and which go in the supplementary file, having a clear message from the outset will answer this question and keep the figures relevant to the rest of the paper! I would also say it’s good to have an idea of what journal you want to submit to at an early stage. A lot of journals have different limits on word count, figures or even references, so it’s best to bear this in mind and avoid any late-night formatting!

You can keep up to date with Will’s research by following him on Twitter @Will_Johnston97. The above publication can be accessed at the following link (https://pubmed.ncbi.nlm.nih.gov/33963212/)

Blogpost by Dr Jason L Brown, Postdoctoral Representative for OMIG.

If you want get involved in these blogposts and promote your research to the OMIG community then please get in touch via Twitter (either via @OMIG_BSODR_UK or my personal Twitter @JasonLBrown1991), or email me on jason.brown@glasgow.ac.uk

JUNE BLOGPOST – ECR discussion with PhD student, Sophie Mountcastle

For our second ECR discussion blogpost, we have Sophie Mountcastle, a final year PhD student at the University of Birmingham. Sophie will discuss her current research and recent publication in npj Biofilms and Microbiomes looking at creating “an open-source tool” for assessing biofilm viability from confocal microscopy images.

Sadly, Sophie didn’t have any action shots from in the labs!
  • Who are you and what is your background? where you are from, qualifications, current position etc.

My name is Sophie Mountcastle, and I am a final year PhD student about to enter my thesis write-up stage. I am part of the Physical Sciences for Health Centre for Doctoral Training (CDT) at the University of Birmingham. At our CDT, physical scientists, computer scientists and engineers apply their knowledge to biomedical challenges, with a focus on interdisciplinary training. I have a background in Chemical Engineering and an MSc in Physical Sciences for Health. Throughout my PhD, I worked in both the School of Dentistry and the School of Chemical Engineering.

  • What is your current research on? Can you discuss the key findings from your recent publication?

Biofilms account for up to 80% of implant-related infections as, unintentionally, medical and dental implants provide excellent surfaces for formation of these 3D bacterial communities. Compared with planktonic bacteria, those present in biofilms can survive harsher environments and demonstrate increased resistance to antimicrobials.

My PhD research is centred around the concept of the “race to the surface” (as seen in the above poster presentation!). This describes the contest between host tissue cells and foreign bacteria for an implant surface. If the battle is won by the host cells, then the surface becomes occupied, and the body’s natural defences can eliminate any bacteria still present. However, if bacteria can colonise the implant surface without intervention, then the subsequent infection can result in significant tissue damage and has the potential to lead to systemic illness.

I’m particularly interested in dental implants because of the unique environment in which they sit, coming into contact with several tissue-types and hundreds of bacteria species. Infection is fairly common, with around 20% of patients developing the disease peri-implantitis within 10 years of implant placement. To tackle the problem of dental implant infection, novel materials and antimicrobial approaches are being developed. However, they aren’t being translated into clinical practice due to a lack of sufficiently representative models to test them adequately. The main goal of my PhD was to develop a way to investigate the interaction between the oral mucosa (gum tissue), oral biofilms, and a dental implant material in vitro.

As part of this work, we realised we needed a reliable way to quantify the formation of biofilms on implant surfaces. In our research group, we regularly use confocal laser scanning microscopy (CLSM) in combination with live/dead fluorescent staining to visualise biofilms. CLSM selectively excites fluorescence signals from different planes within a sample, acquiring images point by point with localised laser excitation at specific wavelengths. CLSM is a useful technique as it enables 3D visualisation of biofilm structure by excluding signals from adjacent planes. Importantly for our work, CLSM combined with viability staining provides high sensitivity, specificity, and resolution.

However, it is very challenging to quantify the number of live and dead bacteria in CLSM images. Manually counting bacteria in an image is very time consuming and makes it difficult to conduct large studies with high sample numbers. Furthermore, while there are a range of image analysis methods and software available in the literature, these approaches are not always accessible if the reported methodology lacks detail. The current suite of image processing tools available for biofilm analysis is difficult to access and cumbersome for non-specialists with no significant programming experience.

Our goal was to develop a simple, automated method to quantify the viability of biofilms stained with SYTO® 9 and propidium iodide (FilmTracer™ LIVE/DEAD® Biofilm Viability Kit, Invitrogen, USA). Written in the open-source software Fiji (ImageJ, U. S. National Institutes of Health, Bethesda, Maryland, USA), we developed a tool called “Biofilm Viability Checker” that can calculate the percentage of viable cells from a confocal image and output the results in a .csv file. Full details on how to implement the tool is provided in our recently published paper and accompanying supplementary information.

The Biofilm Viability Checker has several advantages. It can analyse multiple images at a time, making it easy to calculate and plot the results of a large study. It can also produce images outlining the green (live) and red (dead) cells so that users can check it is accurately identifying the area of fluorescently stained bacteria (below figure). Finally, the time taken to run the image analysis on 25 CLSM micrographs is less than 10 minutes, making it considerably quicker than manually analysing the same images.

Sample images of a variety of biofilms demonstrating the result of automated image analysis using the Biofilm Viability Checker. The green outline indicates the total bacteria area, and the magenta outline indicates the dead bacteria area. (A) Streptococcus sanguinis, (B) Pseudomonas aeruginosa, (C) multi-species biofilm consisting of Fusobacterium nucleatum, Actinomyces naeslundii, Streptococcus gordonii and Porphyromonas gingivalis, and (D) Lactobacillus casei.

A unique aspect of this work is our use of translationally relevant case studies to trial the automated image segmentation protocol, the results of which were also presented in our paper. For example, we used the Biofilm Viability Checker on biofilms of Streptococcus sanguinis and Pseudomonas aeruginosa treated with a commercial mouthwash and demonstrated that P. aeruginosa showed resistance.

  • Where there any unusual results from the study? Any challenges etc that you struggled to overcome?

We felt it was very important to validate the results of the Biofilm Viability Checker in several ways to ensure it would function reliably once published. To do this, we used the tool on bacteria species of different morphologies, including a multispecies biofilm (above figure). We also conducted a sensitivity and specificity analysis, which compared the automated results with manual segmentation. Finally, we checked it gave accurate results on images of dead biofilms to ensure it could handle a wide range of conditions. Setting such high standards for validation was very challenging, as every amendment we made to our tool meant we had to re-run all our checks! However, it ultimately gave us a lot of confidence in the Biofilm Viability Checker when we submitted it for publication, and ultimately, I think it contributed to the paper being accepted.

  • What was the publication process like? Would you recommend the NPJ biofilms and microbiome journal and publish with them again? Any challenging reviewers comments?

The overall process of publishing with NPJ Biofilms and Microbiomes was very good. The journal had great communication with us and were flexible with regards to the impact of COVID-19 on our ability to respond to reviewer comments. The time from first submission to final publication was also reasonable, taking around 8 months.We did receive some strong criticism from Reviewer 2, which was disheartening to read at first and quite challenging to respond to. However, we found that their feedback, along with the other reviewers’ comments, did help us to make the message of the paper clearer. Following their comments we also significantly improved the Biofilm Viability Checker to make it more user friendly and we are really pleased with the final outcome. It has taught me that very tough reviews can have good consequences!

  • What are the next steps with regard to the study? Are any further papers in the pipeline…

The Microbiology Group at the School of Dentistry are continuing to use the tool we developed, and I’m certain it will lead to some exciting new findings in the near future! We hope that the Biofilm Viability Checker will ensure image analysis is an accessible option for those in the wider microbiology and biomaterials fields working on the problem of biofilm-related infection. We will also continue to improve the image analysis tool as we get more feedback from other users.

To access the Biofilm Viability Checker, visit: https://github.com/sophie-mountcastle/Biofilm-Viability-Checker. We welcome feedback from users who apply the Biofilm Viability Checker in their own research. Please get in touch with Dr Sarah Kuehne (s.a.kuehne@bham.ac.uk).

  • Any tips to new research Master’s or PhD students on getting their work published?

I have a few tips that helped me throughout the publication process:

  1. Before starting: Have an idea of the journal you want to publish your work in. This will help you to tailor your narrative to their audience. Make sure to look at their requirements and formatting style and incorporate these into your draft – this will save you time when you come to submit everything!
  2. While writing: Sitting down to a blank document is very daunting. I didn’t write my paper in order! I started with the results and discussion, then went back and wrote my introduction and methods. Furthermore, when writing the first draft of your paper, know that it doesn’t have to be perfect! The first draft is not the finished product, and you will receive lots of input from your co-authors and supervisors.
  3. After submitting: Be prepared to receive some major revisions! It is rare that someone’s first paper is accepted with minor comments. However, don’t be discouraged by the critiques as ultimately it will make your work significantly better. I personally found that taking a few days between first reading the reviews and writing a response really helped me tackle them with a positive attitude!

Finally, expect the whole process to take a long time! It can take over a year (even several) from first coming up with a concept for a paper and finally seeing it published. Persevere and it is well worth it!

You can keep up to date with Sophie’s research by following him on Twitter @sophie_mountie. The above publication can be accessed at the following link (https://pubmed.ncbi.nlm.nih.gov/33990612/)

Blogpost by Dr Jason L Brown, Postdoctoral Representative for OMIG.

If you want get involved in these blogposts and promote your research to the OMIG community then please get in touch via Twitter (either via @OMIG_BSODR_UK or my personal Twitter @JasonLBrown1991), or email me on jason.brown@glasgow.ac.uk

SEPTEMBER BLOGPOST – ECR discussion with BSODR prize winner, Hannah Serrage

For our next ECR discussion we will speak with Dr Hannah Serrage, a Postdoctoral Research Associate at the University of Bristol. Hannah recently won the OMIG bursary fund sponsored by NBIC prize to present her work at the annual BSODR conference held in Birmingham on the 1st to 3rd September, 2021.

Hannah working hard at the Bunsen!
  • Who are you and what is your background? where you are from, qualifications, current position etc.

Hello, I am Hannah Serrage! I am currently a postdoctoral research associate at the University of Bristol, but I am originally from sunny Manchester. I undertook my undergraduate studies in Biomedical Sciences at Newcastle University. At Newcastle, I worked as a laboratory assistant (which involved pouring lots of agar) in the oral biology laboratory and then proceeded to undertake my dissertation characterising receptors on the surface of oral cell types, gingival fibroblasts. After obtaining my undergraduate degree in 2015, I moved to the University of Birmingham to complete my PhD in oral biology examining the anti-inflammatory properties of blue light on oral derived cell types. I received my PhD in 2019 and moved to Bristol, where I am currently exploring the role of extracellular DNA in oral biofilm formation within the oral microbiology group. 

  • What did you present at the recent conference? Can you discuss the key findings/take home messages from your talk (in Layman terms, and in a bit more detail to an expert)?

As part of the Senior Colgate Prize session, I presented work exploring the role of extracellular DNA (eDNA) in oral biofilm formation. The oral cavity is home to a wide range of microbes. Those microbes that colonize the teeth form a thick sticky film known as dental plaque or oral biofilm, the key virulence factor in oral diseases including gingivitis (swollen/bleeding gums).

Oral biofilm formation is initiated by bacterial species (including Streptococcus sp.) sticking to the tooth surface, which then recruit other bacterial species into biofilm. As formation progresses, bacterial species produce and encase themselves in a rich sticky matrix known as extracellular polymeric substance (EPS). EPS comprises a network of molecules that include eDNA.  eDNA has proven an important structural component of oral biofilm that provides protection against antimicrobial compounds. eDNA is seen as an increasingly attractive target for management of oral biofilm development, and application of DNA degrading enzymes known as DNases to early oral biofilm induces biofilm dispersal or shifts in biofilm composition. Interestingly, extracellular DNase activity has been reported for a range of species abundant in oral biofilm. For example, Streptococcus gordonii expresses Streptococcal Surface Nuclease A (SsnA). However, it is unclear as to whether these DNases modulate eDNA networks and subsequent community development.

A major challenge to eDNA studies is the lack of reliable and reproducible methods for assessment of eDNA within oral biofilm. Current methods rely on use of DNA extraction and quantification techniques, which provide no insight into the structural complexity of eDNA. Microscopy approaches have also provided evidence of the ‘web-like’ networks of eDNA. However, there are no tools available to reliably assess the structure and abundance of eDNA networks across oral biofilms.

My project aimed to address this gap through development of an automated microscopy-based tool for the quantification of eDNA networks within oral biofilm. Widefield microscopy was used to visualise fluorescently stained ‘web’ or ‘constellation-like’ eDNA networks within S. gordonii biofilms (Left panel, Figure below). A high-throughput image analysis tool was then used to reliably detect and quantify eDNA structures within images (indicated as coloured lines, where different colours show different points of origin for each eDNA structure, Right panel, Figure below). Information regarding structure and abundance was then output as an excel file.

This tool was then applied to provide evidence that SsnA diminished total eDNA networks within S. gordonii biofilm. Indicative of the role of DNase enzymes in modulating eDNA network abundance. The study was then extended to mixed oral biofilm, using models comprising either three/six bacterial species (S. gordonii, Fusobacterium nucleatum, Porphyromonas gingivalis ± Actinomyces oris, Veillonella dispar and Prevotella nigrescens). These species were selected based on their ability to interact and promote oral biofilm formation. While S. gordonii was the predominant component of each of the biofilms, levels of eDNA were significantly diminished in the presence of other bacterial species. These effects were not related to modulation of SsnA activity. Rather, microbes such as F. nucleatum, P. gingivalis or P. nigrescens may have the capacity to directly remove S. gordonii eDNA or to prevent its release. Where, this study also provided evidence of the DNase activity of these species.

Taken together, these studies demonstrated how a microscopy-based approach can be used to assess eDNA networks within oral biofilm communities. Use of this tool provided novel insight into the biofilm composition dependent modulation of eDNA networks. Where DNases expressed by residents of the oral microbial community may modulate eDNA abundance. Going forward, greater understanding of the interplay of eDNA networks and DNases during biofilm development is required. These DNases may then be exploited as a target to promote the maintenance of an oral biofilm predisposed to oral health.


Visualization of eDNA in S. gordonii biofilms at 5 h. WT S. gordonii biofilms were grown at 37 °C in YPTG on saliva-coated 24-well plates for 5 h. Networks of eDNA were then immunolabelled and visualized by widefield microscopy (left panel). Image analysis software was used to detect and quantify eDNA strands, as shown in (right panel). Representative images are shown. Scale bars, 50 µm
  • What are the next steps with regard to your studies? Has the work been/will the work be published that you were presenting?

I hope the data I presented at BSODR will be published in future but, this is currently a little way off! I We’ve recently discovered that diminished eDNA levels within mixed biofilm communities are due to elevated levels of DNase activity. However, we are currently unsure which species are contributing to this elevation. Using our novel imaging tool, I am exploring the dynamic interplay between DNase enzymes and eDNA networks within oral biofilm communities of varying complexity. With the hope these interactions can be exploited as a target for management of oral biofilm.

Aside from these studies, we have published a review evaluating the role of eDNA in oral biofilm where we summarise mechanisms of eDNA release from bacterial species abundant in oral biofilm. We also highlight shortfalls in current eDNA studies, where reliable and reproducible methods for assessment of eDNA structure and abundance remain lacking (https://doi.org/10.3389/froh.2021.640129). A second publication is also in the pipeline showcasing our novel microscopy technique and its capabilities, so keep your eyes peeled for that one! 

  • How did you find the BSODR conference in general? What was your favourite part?

I really enjoyed it! It was so good to be able to speak with people within the dental research community after such a long time away. I thoroughly enjoyed the OMIG session on Wednesday morning which showcased such a wide breadth of research. I also enjoyed the ECR breakfast on Thursday morning. This provided me with the opportunity to network with individuals at the same career stage as myself. 

  • Given you won the OMIG bursary…. Any tips for MSc students/PhD students/ECRs for writing such applications? 

Well, my top advice would be to just…go for it! However, if I had some more specific advice, it would be as follows:

  1. Really consider why you are applying for this bursary; how will it help you? For me, attending BSODR provided me with the opportunity to showcase my research, gain feedback and network with the ECR community.
  2. Be snappy! Ensure you are concise with your vocabulary and your piece is well structured.
  3. Again…go for it!

Blogpost by Dr Jason L Brown, Postdoctoral Representative for OMIG.

If you want get involved in these blogposts and promote your research to the OMIG community then please get in touch via Twitter (either via @OMIG_BSODR_UK or my personal Twitter @JasonLBrown1991), or email me on jason.brown@glasgow.ac.uk