Rob Finn – EMBL

Welcome to the “Blue Biome Boffins” Campaign where we interview different participants in the BlueRemediomics project, from Early Career Scientists to Senior Researchers, to learn more about their role and valuable work in making this project a success.

To kick the campaign off, we sat down with Rob Finn, co-coordinator of the BlueRemediomics project and leader of EMBL-EBI’s Microbiome Informatics team. In this interview, we talked about Rob’s role as BlueRemediomics coordinator and how he learned to combine his love for microbes with a passion for computing, which led him to his current career path.

Dr Rob Finn leads EMBL-EBI’s Microbiome Informatics team, which is responsible for the MGnify resource, a tool that allows researchers to submit, analyse, discover and compare microbiome data. Rob also has a small research group that probes the functions of microbial ‘dark matter’. Previously, Rob worked with the Janelia Research Campus in the US, where he led a group that designed fast, web-based, interactive protein-sequence searches and annotations. Rob’s academic background is in microbiology, and he holds a PhD in biochemistry from Imperial College, London.

How did you get interested in the field of microbiology and biochemistry?

Rob Finn: I’ve always had an interest in nature and its surroundings. Through my high school years and early university years, I found microbes especially interesting. Combining this interest in microbes with a bit of a misspent youth playing around with computers led me to where I am now.
When I first started my career, there was no mixture of biology and computing. They were two very different disciplines. Since then, computing has become more influential in what we do in everyday life. The fields of biology and computing have merged, allowing us to use computers to understand biological processes, e.g. by cataloguing data to try to understand the biology and biochemistry that they perform. That’s the niche that I’ve been able to occupy – combining these two disciplines.

That’s fascinating. Can you explain your role in the BlueRemediomics Project in simple terms?

Rob Finn: Absolutely. As you may know, there have been lots and lots of people who have sampled the world’s oceans. If you take a cup of seawater, there are millions and millions of microbes in that cup of seawater, even though you can’t see them. So, one way we use to try and understand which microbes are present and to access those microbes is through DNA sequencing. For the BlueRemediomics project, my team gathers all sorts of datasets and aggregates the microbiome data from those various sources into a centralized database. Our aim is to make this database accessible for other scientists as part of the project in a very consistent way so people can access the data at scale and analyse it effectively to get the information they are looking for.
But my role in BlueRemediomics its not only related to us generating data, it’s also about incentivising the project partners to provide us with data from their experiments to have this “central hub”. We can then feed the outputs of the data gathered in the experiments back into the resource to try and improve our understanding of what these microbes are doing and how they can be used for applied settings.

The MGnify platform serves as a database researchers can use to submit, analyse and compare microbiome data. It is also a huge part of the work that you’re doing in BlueRemediomics. What are your goals for this MGnify platform in the next few years?

Rob Finn: We aim to make Magnify a global hub for understanding microbes in various environments, not just the ocean. The microbiome is really important for our own health too. The human gut microbiome is quite a hot topic that people are becoming increasingly aware of. So MGnify is very much designed to become a global hub for understanding microbes that have come from any environment. With this resource, we can process any microbiome data systematically, and then make it available to infer greater knowledge.
Especially interesting in relation to this is that in the past, we’ve only been able to use “signatures” to work out specific segments of DNA, this barcoding or so-called PCR is what most people would have possibly heard about. But now we’re at a point where we can access the entire genome by sequencing the whole DNA that makes up an organism and thus reconstruct the genome of these organisms. This allows us to understand what the organisms are doing in a much more systematic way. Once we’ve got these large collections, we can then start looking at which organisms occur together and form communities that are important. At the same time, we can also see cases where some organisms are never found together, where they’re probably excluding one another.

That sounds interesting! Especially as the human gut microbiome is recently getting more and more attention.

Rob Finn: Yes, I think these disciplines are united by the fact that both, the microbiome found in humans and in the ocean, are incredibly important for the key process associated with that ecosystem’s health. Yet at the same time, they can also be detrimental, or cause disease to their environments. That’s why this question of understanding what constitutes a healthy ecosystem and what we can do to bring it back to a healthier status if it does become diseased, is a very interesting one!

Coming back to your personal interests, what are your personal primary research interests within marine microbiology?

Rob Finn: It’s hard to put my finger on one specific area. I like this holistic view of trying to understand all the microbes that make up a marine environment rather than focusing on one specific area like bacteria, viruses, or small eukaryotic organisms. So for me, it’s that holistic approach of how we can gather important data and start asking key questions. I’m really interested to see how we can use what I would call “nature’s bioengineering”. Microbes are fantastic at adapting and the question of how we can harness this capability to address some of our societal problems is a very interesting one. For instance, when we’re talking about issues such as plastic pollution in the world’s oceans, or the build-up of pollutants within a marine setting – we could actually use those microbes to repair marine environments.

Have you discovered any important milestones or breakthroughs as part of your research related to BlueRemediomics?

Rob Finn: One of the reasons why we have big projects such as BlueRemediomics is to put scientists from different fields together. It’s going from my world, which is very much that computational and data world to then having people take that data forward and start looking at it in an applied setting, such as for drugs, food preservatives and things like that. I think we’re currently beginning to realise the potential, but to translate this potential into products or processes that end users can use takes a lot of time. We have some great opportunities that look like they’ve got great potential, and the longer aspiration of the project is to see how big that potential is – first from a computational point of view, and then by looking at translating it into a larger scale setting to enable society to take advantage of those outputs. One aspect I personally find very interesting is the plastic degrading enzyme we are looking at, but it’s tricky to scale it up so far. We can definitely find enzymes that can break down a typical water bottle but they’re currently very slow and not profitable. We’re currently taking the small steps along the way to find out how we can improve the function of those enzymes in such a way that it becomes maybe a 3-day process instead of a 3-week process to degrade a plastic bottle. Related to that, a question that will need to be answered is how we can make this cost effective compared to more conventional ways of recycling.

We had an ethics discussion about microbiome manipulation before. Do you see any issues for instance with plastic degrading enzymes in terms of how these enzymes might manipulate the marine ecosystem if they were employed?

Rob Finn: In this case I don’t see an issue as the application of such enzymes would be in a very controlled setting, where the plastic would be put in “silos” to degrade back down into its basic building blocks. The ethical question comes in when you’re planning to produce microbes or enzymes to put those back into an environmental setting. For instance, there have been suggestions of doing that to tackle the large amounts of microplastics floating around in the ocean. The question that arises when you’re dealing with a live organism is, how are you going to control it? Even if it’s just an enzyme, how do you know what potential impact it will have to break down other things that you hadn’t tested for or anticipated? I think we have a huge responsibility as scientists not to overhype, but when we do make these discoveries to really think about how they could be deployed without harming the environment. One of the future topics, I believe, is this notion of how viruses may control algal blooms. Now, an algal bloom, you can’t take out of a marine setting. Algal blooms have a very negative impact on both the environment and society. The question is – would people be happy if we started spraying these algal blooms with a virus? And that leads us back to the question: do we understand the side effects? Can we control that virus and stop it in some shape or form? I think that’s where much longer-term research is needed to really understand those problems, because they are not easy to answer.

Where do you see yourself after the BlueRemediomics project is finished?

Rob Finn: Having a rest somewhere is on the top of my list, it’s very busy and very time consuming. Aside from my holiday plans, there would be aspects of this project that we would hope to take forward to potentially build new projects, based on the resources we have built in BlueRemediomics. The aim is for scientists beyond the BlueRemediomics consortium to become more familiar not only with the potential of the marine microbiome, but also with the data and resources we provide. At the same time, we also aim to make the general public more aware of the importance of marine ecosystems and the role of microbes for ocean health.

BlueRemediomics: As the last ending question, can you tell us one thing about marine microbes or microbiome data that most people wouldn’t know?

Rob Finn: That’s a tricky one. Maybe most people already know this, but here’s an interesting fact: everyone thinks that the oxygen we breathe, which is vital for our existence, is largely produced by rainforests. In reality though, the world’s oceans are responsible for over 50 percent of the world’s oxygen production!