Focus on research: Dr Pauline Scanlan, APC Microbiome

Pauline Scanlan, APC Microbiome
Pauline Scanlan, APC Microbiome

Looking at micro solutions to macro problems



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21 December 2020 | 0

Dr Pauline Scanlan is based at APC Microbiome Ireland, the Science Foundation Ireland centre for research exploring the role microbes play in health and disease.

She is also a two-time recipient of a Royal Society-SFI University Research Fellowship. In this interview she talks about her roundabout academic career and the importance of STEM outreach.

Your academic career is a bit of a case of ‘Cork and back again’.

Yes, very much so. I started my studies in Cork and I now have a permanent position here, but I have been lucky to take a few detours en route.




I first came to Cork as an undergraduate student and graduated with a BSc in plant & microbial biotechnology. I then continued my studies with a PhD in medicine, during which time I spent a year at Wageningen University in the Netherlands.

Following my PhD I then moved to the University of Oxford which was a very formative experience for me as a scientist. Here, I got the opportunity to work in a world-renowned research group with an exceptionally talented supervisor who really saw my potential and instilled in me the independence and confidence to start writing my own research grants and pursing my own research ideas. It was an international lab, we worked hard but also enjoyed our time off and I am happy to say that many of us are still in regular contact.

In 2013, I was awarded a Marie Curie Fellowship to return to Cork, this time at Teagasc, Moorepark, Fermoy. Then in 2015 I was awarded the RS-SFI URF to move my research to APC Microbiome Ireland, UCC. It has been a very busy and exciting few years, but I love living and working in Cork and now that I have started a family here it is good to put down some roots.

Your work has something of a topical element in that it looks at the effect of viruses on the microbiome. Can you take us through it?

As part of my research, I work on bacteriophages which are viruses that infect and can kill bacteria. I am interested in understanding how bacteria evolve or change in the human gut and we know that bacteriophages play a really important role in this process.

Bacteriophages can drive the evolution of their bacterial hosts in a number of ways, but the most common route is through integrating their genome into the bacterial genome. In doing so, they carry novel genetic material with them which can give their bacterial host novel functions. These functions can be detrimental to the human host as sometimes bacteriophages carry what are called ‘virulenc’e genes which encode proteins that can cause disease in the human host. Conversely, these bacteriophages may carry with them genetic material that encode functions that provide bacteria with functions that are beneficial to the human host.

Although we do not know very much about these processes in the human gut and this work is very much in its infancy, it is very exciting to work with microbes such as bacteria and phages as we can watch them evolve in real time in the lab. This means that I can isolate bacteria and phages from the human gut and study evolutionary processes in the lab and in great detail.

I am currently one of a handful of researchers worldwide investigating real-time evolution in the human gut microbiota. This research is important for many reasons but particularly because a central goal of gut microbiota research is to link bacterial diversity to function and ultimately host health.

However, if bacteria can rapidly evolve to perform different or novel functions in the human gut over short periods of time this has many implications for our understanding of the role the gut microbiota plays in human health, as well as our ability to predict how the microbiota impact on both health and disease.

On a side note, many researchers are interested in bacteriophages for their therapeutic potential. Lytic bacteriophages cannot integrate into bacterial hosts genomes and instead kill their host almost immediately upon infection. Lytic phages have been used for almost a century to target bacterial infections in some parts of the world (eg Eastern Europe and Russia) and although phages largely fell out of favour as an anti-bacterial therapy when antibiotics were discovered and began to be mass produced this research area is now undergoing a renaissance. This is largely driven by the rise and spread of antibiotic resistance microbes that have emerged as a major threat to public health. Here, bacteriophages are being mooted as one solution to combat microorganisms that have become resistant to conventional antibiotic therapies.

You’ve spoken about the challenge of securing samples and generating data for publication within the bounds of a 2-3 year grant. Does this have a negative effect on what areas researchers choose to investigate?

Sample collection can be very difficult, but it depends on the type of sample that you want. Most samples are ethically sensitive so you have to apply for permissions to work on them which can take some time. Then if you need a large number of samples to work with, it takes even longer to recruit the number of people required.

Other samples, such as intestinal biopsies, are medically invasive to acquire so you need to collaborate with clinicians to access them. So yes, sample collection can be challenging and can affect your ability to address certain research questions with the power and sensitivity you would like and also within the timeframe of a grant. As such you sometimes have to tailor your research questions and experimental design based on your sample set – which is not always ideal.

From a career perspective, how has your latest award helped develop your research, teaching and outreach efforts?

It has been hugely beneficial, particularly from a research perspective. The award is dedicated to discovery-based science so all other activities in principle should be secondary and we are expected to dedicate most of our time generating novel and hopefully exciting data that pushes the boundaries of current knowledge in our research field. I try to spend as much time as is possible in the lab but I am also committed to teaching, student supervision and mentorship.

I also think that the award was key to me securing permanent lectureship at the School of Microbiology where I do some teaching and supervise students in the lab, as well as being involved in a couple of mentorship schemes within UCC.

My Institute is very active in outreach and I usually engage with four or five activities per year, such as Science Fest or hosting students in my lab to give them hands-on work experience.

What directions in microbiome research are you finding exciting right now?

I started working on the gut microbiome in 2002 when it was very much a fledgling field and have since seen many advances in the technologies and methodologies used to analyse this complex community of microbes. The increased awareness of the fundamental and pivotal role our microbiota plays in health has really intensified research in this area.

Over the past decade gut microbiota research has really broadened its horizons and is now linked into physiology, nutrition, medicine and neuroscience just to name a few. The advent of low cost and high-through-put sequencing technologies has greatly accelerated data generation in microbiome science and this has allowed us to get a very detailed insight into how the gut microbiota varies between different human populations and according to age, health status, disease group, diet and so on. However, what we need now is a better understanding of how variance in genetic diversity encoded within the gut microbiota affects human development, physiology and health.

One exciting area that is emerging and is potentially revolutionary is the use of artificial intelligence and machine learning to analyse complex multidimensional datasets that include detailed information on the gut microbiome as well as the human host. One very useful output from this type of analysis would be the identification of early biomarkers of disease processes that are linked to the gut microbiota which would help develop novel diagnostics as well as intervention and/or preventative strategies.

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