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Q&A: New JGI Director Discusses Plans to Engage With Industry, Focus on Systems Biology

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SAN FRANCISCO (GenomeWeb) – Nigel Mouncey joined the US Department of Energy's Joint Genome Institute in March as its new director, following the retirement of Eddy Rubin, who served as director for 14 years. Mouncey joins JGI with around 20 years of experience working in industry, most recently as the research and development director for bioengineering and bioprocessing at Dow AgroSciences.

In his new position heading up JGI, Mouncey said that he wants to engage more with industry researchers, getting them involved in the institute's community science program, as well as tap industry for sponsored research.

In addition, he said he is looking forward to collaborating more closely with the other San Francisco Bay Area-based DOE labs, like the Lawrence Berkeley Laboratory and the SLAC National Accelerator Laboratory at Stanford. An upcoming move by JGI from Walnut Creek, California to a new facility at the Berkeley Lab — the Integrative Genomics building — in 2019 will further enable closer collaboration. As has been the case over the last several years, JGI is increasingly moving beyond being a sequencing service provider, and is focusing on providing technologies that enable more systems-level biology — understanding how sequence impacts function and structure. In addition, with growing amounts of sequence data, JGI is looking to develop technologies to better analyze that data. 

The following interview with Mouncey has been edited for clarity and length.

Can you describe your background and what led you to make the switch from industry to JGI?

Throughout my industrial career, our objectives have been to harness the power of biology and microbiology using microbes to produce a whole range of different products for food, feed, agriculture, plastics, and even cosmetics. All that work has been founded on developing a fundamental understanding and … translat[ing] that into optimizing strains and fermentation processes that enable high yield, high rate, and pure production of atomic molecules.  

I've always loved working with state-of-the-art technologies. The area of genomics is still undergoing this incredibly fast development of technology — ways to understand more complex genomes, really being able to interrogate those and gain understanding. That can be translated to the application side of things. JGI is really at the forefront of this, so it's an exciting time to be more involved in this space today, than it was in industry, and it's an exciting time to be at JGI.

What is your vision for JGI and how do you think your industry background influences that vision?

JGI has gone through a major evolution since its founding as one of the human genome sequencing project centers in 1997. It became a Department of Energy user facility in 2004 that focused on providing infrastructure for researchers working on DOE mission areas of bioenergy, carbon cycling, biogeochemical cycles, and providing sequencing technologies for that. Today, we're post-sequencing and putting more emphasis on genome science to infer function from genomes and genes, and integrating different technologies that allow us to do that at a scale that few others are able to do. The vision for JGI is to continue that evolution into an integrated genome science user facility. 

Do you plan to implement any different programs or projects?

I'm developing a framework right now for our industry engagement program that we hope to launch this summer. We'll take that to different potential industry partners so they can take advantage of our technologies to help with the fundamental understanding of the work they're interested in as well as provide another means for us to grow our technical capabilities.

We want to grow our user communities. It's been quite apparent to me that while we have a fabulous user community today there are a lot of people out there that don't have a great awareness of what JGI's capabilities are, what we can offer. So, we are expanding our outreach efforts to really try to attract new users and user communities.

What types of industries are you looking to engage with?

Being a DOE user facility we're certainly looking at those industries that are involved in energy and the environment. I think we'll probably, at least in the near-term, not talk with people in the health industry. A lot of it will be around the industrial biotech industry, potentially the ag industry as well, and maybe some of the companies that are involved in biomaterials that I think could fit in within the grand mission.

How would those types of collaborations work? Would it be a fee for service type model?

We have our community science programs and there's nothing preventing industry from participating in those. They'd be subject to the same open sharing of data that those programs offer the user communities. That's one angle. The other is through strategic partnership projects or through something that's called cooperative research development agreements. These types of agreements are much more geared toward sponsored research and have the usual terms and conditions that you find with those things. That could be fee-for-service or a much more collaborative effort. We prefer cooperative development research agreements where we're science partners with them. That iterative science and communication I think is really the most beneficial way to advance science and technology. 

What research areas will you be most focused on?

We have a wide variety of sequencing platforms and so can sequence pretty much anything today. But, now, we're going into deep sequence to get to levels of the biological universe that haven't been seen before. For instance, microbial dark matter — exploring microbes that haven't been identified before.

We have a growing program in environmental viromics to understand more about viruses. The numbers are that there are 10 viruses for ever microbe out there. It's a very unexplored space. Viruses are being shown to play really important roles in the environment, but that space is very untouched. So, on the one side, we're continuing to sequence, but sequencing much more of the unexplored world.

Also as we continue to grow sequencing, we are developing and employing novel methods to analyze the sequence data. It's very big data; huge amounts of data. We need new ways to be able to process that faster and at a deeper level. We have a fantastic partnership with [the National Energy Research Scientific Computing Center] (NERSC). Something that really excites me is our ability to readily access this high-performance computing environment to help us process the data. That's both for assembly and annotation of the sequence information.

But, I think today where we're really trying to grow JGI is in developing new technologies that we can provide to users in the community on things like DNA synthesis science and on high-throughput metabolomics that allow us to recapitulate biological systems in host organisms that are easier to cultivate. Then, we can use things like metabolomics and proteomics and get more insight into gene function, not only in isolated genes, but pathways and biologically relevant systems with an ultimate goal of trying to gain a systems-level understanding. 

Are there specific issues within bioenergy that you're looking to tackle?

We are working on our plant and plant microbe programs to better understand how you can grow feedstock crops sustainably in conditions that are not optimal, like drought, low-nitrogen environments, or environments where you have very low or high radiation from sunlight. The role that soil microbiome plays in those conditions is something we're really exploring. And how to break down that biomass efficiently and effectively in a way that opens up the sugars that you require for the post feedstock conversion to fuels and chemicals is a big area for us. We're doing a lot of work in biogeochemistry and nutrient cycling to better understand environments and how those are changing over time and how you then can manage those in a more sustainable way.  Those are probably our two big areas right now.   

Do you see any major shifts in direction for JGI?

JGI will be moving on the continuum of this evolution toward structure-function relationship science. For example, we have this amazing amount of diversity of enzyme sequences in our databases. Take lipases. We have something like 50,000 lipases that span all of the diversity of lipase families, many of which are not really well understood.

We have the ability to work with [the Lawrence Berkeley Laboratory's Advanced Light Source] and [SLAC National Accelerator Laboratory at Stanford University] to address questions using novel ways of doing structure-function work.

For instance, in collaboration with the Berkeley Lab, we're working on using imaging techniques like [cryo-electron microscopy] that can look at not just protein structure, but also host/microbe interactions. There's been some fascinating work that looks at time series of root/microbe interactions.

That's something I'm very keen to continue — ways of bringing new technologies, the partnerships with other national labs, like the Berkeley Lab, to really tap into a lot of structural elements.

What do you see as the major scientific challenges that JGI will have to solve?

The sheer volume of data that is generated today and will continue to grow from DNA sequencing platforms. There's the challenge of being able to process that single type of data. But, I'm really keen to see how we can best integrate different types of data. That is an even bigger computational challenge. This is an area of priority for us — to really work though how we do this. Being able to manage different types of data and the scale that data is growing — to exascale and even beyond to petascale-level data — is a global challenge. That is probably the biggest challenge. 

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