Our Interview with Prof Paul Cotter

Prof Paul Cotter is the Head of Food Biosciences at Teagasc and a Principal Investigator with the large Irish Research Centres, APC Microbiome Ireland, Vistamilk and Food for Health Ireland. He also co-ordinates an EU H2020 Innovation Action relating to microbiomes and the food chain, ‘MASTER’. He is a molecular microbiologist, with a particular focus on the microbiology of foods (especially fermented foods), the food chain (especially dairy production and processing) and of humans (using in vitro, ex vivo, and in vivo approaches) as well as probiotics and postbiotics (including bacteriocins). We caught up with him to find out more about some of his latest research.

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1. What led to your interest in microbiology and particularly microbiology of foods and their relation to health?

I was always very interested in science, even as a second level student in Ireland. When I went to university, the degree that I commenced was a general Biological Sciences degree, and so we were exposed to lots of different types of Biological Sciences in the first two years and then specialised thereafter. There were some lectures relating to Ebola and some very serious diseases that really caught our attention and our imagination. Obviously, those diseases aren't really a big issue in in Ireland, but once microbiology  grabbed my attention, I became aware from our lectures and from my other reading, that Cork has a long history in food microbiology.

So, there was an opportunity there to really stand on the shoulders of giants. There are people like Charlie Daily and Seamus Condon, Gerald Fitzgerald, and more recently Paul Ross and Colin Hill, who really led that field of research. It really intrigued me and I saw there being an opportunity to get involved.




2. One of your interests is food-grade antimicrobials and their application in controlling food spoilage. What are some of the most promising findings within this area of research?

I would say that bacteriocins which are the antimicrobial peptides that you normally think of when thinking of food grade antimicrobials, have been studied for around 18-19 years now. Things like nisin are extensively used in foods, but I still think they are relatively underutilised.

In recent years there's been an increased application of approaches like conjugation especially for the fermented food industry and companies that work on developing new starter strains to mobilise genes associated with bacteria from production into starter strains and adjuncts, or fermented food applications. It's great to see that happening, and that seems to be where a lot of the developments have taken place. I still think that we're not fully harnessing them for food preservation to larger extent. Some of the developments that have taken place with regards to engineering or bioengineering these antimicrobials have been very interesting, and scientists seem to be quite open to changing them to facilitate enhanced activity or different target ranges. But to do that typically involves approaches that are either genetically modified or are quite difficult to do and retain the non-GMO status.

But I think that's something that we continue to evolve but probably won't become commonplace or be used extensively until we hit some sort of crisis or some requirement that the existing food antimicrobials no longer perform the role that is required.

3. We know that ‘fermented foods’ have become a hot topic in research and the media, especially with regards to their effects on health. Based on your research, what are some novel findings around fermented foods and health and what can we expect future research to explore further?

Yes, I think that whole area has attracted a lot of renewed interest in recent years.

In particular, in Western society there had been a move away from fermented foods over the last 100 years or so due to increase reliance on pasteurisation and other approaches that typically made foods sterile or contain very few microorganisms. Fermented foods just lost popularity at around the same time. They have continued to be consumed in other parts of the world and fortunately things are starting to revert here. I think some of the key questions related to just how useful or how beneficial it is to be consuming a diet rich in fermented foods, and indeed more generally live microorganisms (from fermented foods or probiotics) and how they can contribute to your general health.

And things like next generation sequencing based approaches that are better at determining what are the microbes in those foods, what health associated genes they encode and how subsequently they can impact on the gut microbiome and health via that route, is attracting ever increasing interest.

The other approach in my lab and in very many others relates to deconvoluting fermented foods or artisanal fermented foods in a way as these foods are sometimes difficult to scale up or to produce on a consistent basis to make them available to large sections of society.

If we studied the individual microbes here at present and then almost put them back together in a simplified way while still retaining the key health promoting attributes and the key, distinctive features that are associated with the fermented food, then that means they are more easily made commercially. And as I say, that can be done in a way that ensures high quality control and availability to thousands and millions of people rather than a few individuals that happen to have the right fermented food in their kitchen.

4. We heard you’re working on the MASTER project. Could you tell us about the aims of this project?

So MASTER is an EU-funded project that I coordinate and it's an innovation action which means that the research that takes place there should be of the kind that will result in outcomes with a high TRL i.e. a high technology readiness level. And in other words, those products will be on the market, and they may be available for applications to companies in in the next few years. So, it's funded to the tune of €11 million over 5 years and there are 30 different partners from universities and other research institutes but also lots of industries including small and medium sized enterprises.

The idea there is to harness microbiome-based tools and concepts and to specifically apply them for research or for applications relating to the food chain. We have different work packages that focus on marine environment and marine microbiomes, as well as plants and soil, the rumen, food processing, fermentation and human health, and the sort of outputs and products would include probiotics, bioprotectant strains, new bioinformatic pipelines that will be available for people to apply, other standard operating procedures or SOPs relating to how best to examine a particular microbiome, databases so that you can more accurately assign DNA sequence reads. If for example, you're studying your own food processing facility and working with companies like Oxford Nanopore Technologies that develop handheld sequencers so that sequences are not just located in research labs around the world, but eventually you might have a quality control person in a lab in a food processing facility that will be using a minION or another instrument like that in order to assess the microbial quality of their products and their environments.

5. What are some tips you would share with aspiring molecular microbiologists based on your expertise within the field?

I was thinking about this question, and I think the advice I'm going to give is not necessarily focused specifically on molecular microbiologists, but to anybody who's planning their career and deciding what they would like to work on in the future. I guess what I would say is find something that you're passionate about, because if you’re enthusiastic about something and really committed to it, then working on that topic won't feel like work. You'll enjoy it and it will be like a hobby. Once you identify that area that you are passionate about, then really put your heart and soul into it and work hard because there are ways of enhancing your profile and using social media and other outputs, interacting with different people and networking that can help enhance your career. But ultimately, in our field, you need to focus on the science and work hard in the lab in order to underpin all of that. And without that, everything else will not provide the necessary strong foundation to succeed.