An interview with Dr Alan Walker

April 2020

Dr Alan Walker is A Senior Lecturer at the Rowett Institute, at the University of Aberdeen, Senior Editor of Microbial Genomics, and a member of the Microbiology Society. In this interview, he tells us more about his research, which focuses on the intestinal microbiota, and tells us more about the benefits of being a member of the Microbiology Society. 

Alan Walker
© Alan Walker

Tell us about your research

I’m based at the Rowett Institute at the University of Aberdeen and our research is focused on the human gut microbiota, which is the collection of microbes that live inside our guts.

Our particular research angle is to look at the three-way interaction between the food we eat, the gut microbiota, and subsequent potential impacts on host health. We have a pretty good understanding now, from research over many years, of some of the types of gut microbes that will respond to specific dietary interventions. However, less is understood about how promoting these species in the gut might impact health. Our group, therefore, studies some gut bacterial activities that are relevant to health, such as whether or not certain species might inhibit pathogens or produce compounds that might be beneficial (such as anti-inflammatories), or produce more detrimental products that are linked to disease.

Why is this research so important?

There are a few reasons for that. As recognition of the roles that the gut microbiota might play in health and disease has grown, it has drawn in interest from a broad range of research disciplines. This has been a very technology driven process, meaning that research on microbiota, strongly overlaps with many other areas of microbiology, such as microbial ecology, genomics, bioinformatics etc. This means that new understandings and methodologies, to study the gut microbiota, are also relevant for many other fields of microbiological research, and vice versa.

From a public relations perspective, the field of gut microbiota research is also important for microbiology as a whole, as it very much plays towards our sense of self, because we obviously all have a microbiota. The general public has definitely begun to show increasing interest in this area of research, and I think that one of the advantages of this is that it has the potential to help everyone really take more notice of how important microbes can be, and not just think of them as “germs” that cause disease.

Where did your interest in microbiology come from?

I’m a bit embarrassed by the answer to this question, but I will tell the truth! I wish I could tell you like some scientists, that it was a lifelong ambition spurred by natural childhood curiosity, but in my case, it really came about as somewhat of a happy accident.

I actually started off doing my undergraduate studies in immunology and zoology, but I was not really enjoying it. Immunology involves too many acronyms, and I didn’t care about the mating patterns of hyenas, so zoology wasn’t really engaging me either. However, I had a good friend that was studying microbiology, and at the end of second year I decided that if I changed my course to microbiology, I could go to the pub more often with him instead! I’m therefore very ashamed to admit that I initially chose microbiology because it would fit better into my drinking schedule at university….

However, there is some happy redemption at the end of this sorry tale. Once I started studying microbiology, everything really clicked into place for me. I loved the subject immediately, had an inspiring group of lecturers and classmates, and suddenly university went from being a bit of a drag, to something I actively enjoyed. I still love learning about microbes!

What qualifications did you obtain before starting this role?

After I got the aforementioned BSc in microbiology from the University of Aberdeen, I took a job in an NHS diagnostic lab for one year. That year was honestly some of the best microbiology training anyone could ever wish to receive! I processed many, many thousands of samples, and learnt a huge amount of what we would now class as more “traditional” microbiological skills.

Following on from this, I decided to do a PhD in gut microbiology and registered at The University of Dundee. I was really fortunate that I was supervised by three really pioneering gut microbiologists (Harry Flint, Sylvia Duncan and George Macfarlane) at a time when it was considered a smaller and more niche field of study. Then I carried out eight years of postdoc research at the Wellcome Sanger Institute, working for Julian Parkhill’s group, which is where I learnt a lot more about DNA sequencing methods. My time there coincided with the advent and widespread adoption of next generation sequencing technologies, and it was tremendously exciting and inspiring to be in a place where these techniques were rapidly changing what was possible in biology, and all in such a very short space of time.

The current work in our lab combines the modern and traditional methods, which are still hugely relevant and important. We carry out the sequencing-based approaches to do top-down based surveying, but we also use the more traditional anaerobic microbiology culturing approaches to build on those screens by doing more bottom-up, mechanistic work.  The combination of the two really allows us to move beyond purely correlation-based conclusions.

What are the professional challenges that present themselves and how do you try to overcome them?

Academia is a really interesting job. For me, the most challenging aspect is just around managing workload. The PIs I have most admired are particularly effective at problem solving and supporting their team as much as possible. This can be difficult at times, particularly when you have multiple competing demands on your time, but I do my best to try and follow their example.

What is a typical working day for you?

The flippant and easy answer to this question would be; emails and meetings! However, this doesn’t do justice to the role and the variety of tasks we undertake, such as the data analysis/interpretation, the travelling, the writing, the teaching/supervision, as well as policy, editorial, committee and public engagement work. So, whilst on a ‘mode’ average day it’s emails and meetings, throughout the same week you could be undertaking a huge variety of different things.

Tell us about your biggest professional achievement(s) so far.

Rather than talking about my biggest professional achievements, I prefer to think more in terms of the things that have brought me the most job satisfaction. My favourite thing about being a scientist is collaboration, and I have been lucky enough to contribute to novel research alongside literally hundreds of fantastic, inspiring and clever people. It’s a pleasure and a privilege, and I am very proud to have been involved in some really exciting studies.  

You are an active member of the Microbiology Society, tell us more about your involvement.

I first joined the Microbiology Society back when I was doing my PhD and I have been a continuous member ever since. I have gained a lot from it, and I’ve taken a more active role in the last few years since I have become a PI.

My main role as a member is as Senior Editor of the Society journal, Microbial Genomics, which is currently accepting submissions! Journals are an important revenue source for the Society and allows us to put money back into the microbiology community via things like conferences, grants and other activities.

Beyond that, I have been on the organising committee for various Society meetings and sessions, which I have really enjoyed because, if nothing else, it gives you a chance to listen to talks from your favourite scientific groups and learn more about their fantastic research.

Finally, I’m a very enthusiastic meeting attendee, and I try and attend the Annual Conference every year. The conference is a great opportunity to listen to some inspiring science, catch up with old friends, and make new collaborative links.

Why is it important to be a member of an organisation like the Microbiology Society?

There are lots of reasons to be honest! The nicest thing for me is the sense of community, and that you feel that you are a part of a bigger network of like-minded people. The Annual Conference is a great example of that; the chance to network has led to lots of exciting collaborations, and from a social aspect it can be great fun.

The Society also plays an important role in promoting microbiology to the wider public and policy makers, and I am very proud to be a member.

Why does microbiology matter?

Unfortunately, the world is learning right now via Covid-19, that microbiology is fundamentally important. Furthermore, microbiology expertise is needed more than ever to help us tackle hugely important societal problems such as antimicrobial resistance.

Beyond such immediate threats, the main thing I try to get across in my lectures to new undergraduate students is that we are all living on a microbial planet; microbes were here billions of years before us. They play fundamental roles in so many different aspects of the functioning of this planet and they are endlessly fascinating. I am still very glad that I decided to align my university drinking schedule with a microbiologist!

If you are a member of the Society and would like to find out more about how you can get involved with Society activities and/or showcase your research, please email us at [email protected].