Fleming Prize Q&A – Professor Peter Fineran

08 April 2019


Our Prizes recognise excellence and are awarded to those making significant contributions in the field of microbiology, based on nominations received from the membership. They are awarded at our Annual Conference, where the winners also present their lectures. Ahead of the Fleming Prize Lecture, Omololu Fagunwa, a member of the ECM Forum Executive Committee, interviewed Professor Peter Fineran to find out what inspires him, learn more about his work and how it feels to win a Microbiology Society prize.

Peter is also a former Sir Howard Dalton Young Microbiologist of the Year winner (third place, 2006) and recipient of the Society’s President’s Fund (now Research Visit Grant) in 2005.

What does it mean to you to be a Microbiology Society prize winner?

I am really delighted and honoured to receive the Fleming Prize. I have had so many fantastic students, staff and collaborators over the years and our work is really a large team effort. I am grateful to the Microbiology Society for the award and the University of Otago and the Department of Microbiology and Immunology for their support.

Can you tell us about your journey into science?

I guess I was surrounded by science from a young age, having two botanists as parents. I also had some great teachers at school. At primary school we had a teacher called Mr Falloon who would give us all sorts of practical projects that would be competitions - e.g., make a mouse-trap powered car travel the furthest or a marble fall from 1 metre in the slowest time! Mr Falloon and other inspiring teachers really sparked my interest. I recently found a school book from when I was about 9 or 10 which had a picture of a lab and I wrote that I wanted to make “invenchins" (yes, my spelling could have been better). Later, at high school I went through many different ideas of what I wanted to be when I grew up. I eventually did a BSc Hons in Biochemistry at the University of Canterbury in Christchurch, New Zealand. This was a flexible degree; I could do lots of chemistry, biochemistry, genetics and microbiology. I started getting interested in two topics that I would pursue later. I learnt of quorum sensing and thought it was amazing that bacteria could talk to each other. I also did a project on phages and started my interest in these incredible viruses. I think it was during this time that I realised that I really like molecular genetics and that bacteria provided such nice simple model systems to study cellular processes.

I was fortunate to get a scholarship from the New Zealand government to do my PhD at Cambridge with Professor George Salmond. I was attracted to working in his group by his work on quorum sensing and stayed on to work on a post-doc project on a new phage resistance system. I was then fortunate to get a lecturer position at Otago in New Zealand in 2008 to set up my research group. It was just at the time that the first CRISPR papers were coming out and this fitted well with my interests in phages and phage resistance. We have been working on phage resistance systems and gene regulation since then. 

What are your research foci and what are the motivations for going in those directions?

The main aim of my research is to understand the interactions between bacteria, their phages and other mobile genetic elements, such as plasmids. These interactions are hugely important for bacterial evolution, the rising challenge of antibiotic resistance and phage–host interaction are also significant player in global ecology. My lab focuses on phage resistance systems, mostly CRISPR-Cas and toxin-antitoxin/abortive infection systems. My motivations are two-fold. Firstly, we know so little about these interactions when we consider how abundant and ubiquitous they are and their impact on the earth. Fundamental knowledge is required to be able to understand these processes and how they influence life on earth. Secondly, microbes (and particularly phage resistance) has an incredible track record in the generation of biotechnological tools. Our research also aims to take our fundamental discoveries and use that knowledge in ways that can be beneficial.

What do you consider to be your biggest personal and academic achievements?

I am really proud of the work I did during my post-doc with George Salmond and Tim Blower which led to the discovery of Type III toxin-antitoxin systems and showed that this can provide phage resistance via abortive infection (cell ‘suicide’). This is currently my most highly cited work and helped link together two different areas of microbiology (toxin–antitoxin and abortive infection systems).

I also think my lab has made some important contributions to the CRISPR-Cas field. We have made significant discoveries in how bacteria acquire new memories from the invaders during CRISPR adaptation. One process we have worked on extensively is a positive feedback loop called ‘priming’ where spacers that match, or partially match, the invader stimulate a rapid boost in immunity through the acquisition of multiple additional spacers. This makes the defence stronger and harder for the phage or plasmid to escape via mutation.

We have also shown that CRISPR-Cas systems make mistakes during adaptation and that this can result in autoimmunity. These self-targeting spacers can then cause dramatic genomic changes, including the deletion of entire pathogenicity islands. Recently we showed that one-way bacteria might control their immunity by up-regulating it through quorum sensing communication when populations would otherwise be at a heightened risk of a phage epidemic.

I also get an immense amount of personal satisfaction from training other scientists. I must have had over 50 people work in the group in the last 10 years and they are the lifeblood. I feel very proud when I see them learn, develop and succeed.

How have improvements in technology within the last 20 years impacted on your research?

If I look at what has been happening – probably more in the last 10-15 years – the huge amount of data from next generation sequencing has made a big impact. In our recent work, we have been able to sequence millions of new spacers acquired by CRISPR-Cas systems and study aspects of CRISPR adaptation. In my PhD I mapped some transcriptional start sites by primer extension and 5’ RACE. Now we can get every start site in an entire organism in a single sequencing experiment. However, I still think that having good questions and experimental design is the critical part to any study.

How does CRISPR benefit the average person?

Well, if you had yoghurt this morning then you probably had some dairy that has been fermented using strains that have been naturally adapted (using CRISPR) to phages that can spoil fermentations in the dairy industry. So, it is already having an application there. More generally, the tools are leading to massive advances in our ability to do fundamental science and to understand disease processes. We are also heading in the direction of being able to use CRISPR in different therapies and diagnostics.

Do you have any advice for Early Career Microbiologists (ECMs)?

I think that the most important thing is to enjoy what you are doing and have fun. It is a real privilege to be able to work on exploring how the natural world works. I have also benefitted greatly from excellent mentors – my advice would be to seek out mentors. Also, be a mentor to other students or researchers – you will learn a lot through helping and teaching others. There are so many good opportunities, try to take advantage of all that are available. Talking about science is critical – talk in the lab about your work, talk about it over a coffee, talk with new people, the public, meet new people, go to new places, it really is a wonderful job.

This lecture takes place tomorrow at the Microbiology Society Annual Conference at 17:40 in the Main Auditorium.

Inspired by our outstanding Prize winners? Nominations for 2020 Prize Lectures and the 2021 Prize Medal are now open. Visit https://microbiologysociety.org/prizelectures for more information.

Image: Professor Peter Fineran.