Why scientists are teaming up to study the microbiome: A Q&A with Jack Gilbert

Don’t be alarmed, but you are covered in bacteria. So is the device you’re reading this on, and so is your desk, your kitchen, your house, your food … you get the idea. Bacteria, viruses and fungi are everywhere, and the microbiome—the collective population of these microorganisms inhabiting every corner of our world—has a profound influence on human health and the environment.

Scientists are just beginning to understand how these vast ecosystems of microbes operate and interact with each other, and they’re finding tantalizing clues about how they can harness them to create precision medical treatments, better antibiotics, cleaner energy sources and even self-cooling workout clothes.

The University of Chicago and its partners at Argonne National Laboratory have been at the forefront of microbiome research, but no institution can tackle an area of this much complexity alone.. This week, in an article published in Science, 17 U.S. scientists—including microbiologists, physicists, chemists and physicians—announced the creation of the Unified Microbiome Initiative (UMI), an interdisciplinary group that will coordinate areas of microbial research and make funding recommendations to federal agencies, private foundations and corporate partners.

Jack Gilbert, PhD (Photo by Mark Lopez, Argonne National Laboratory)

Jack Gilbert, PhD (Photo by Mark Lopez, Argonne National Laboratory)

Jack Gilbert, PhD, associate professor in the Department of Ecology & Evolution at the University of Chicago and group leader for microbial ecology at Argonne, is one of the founding members of the UMI governing board. Science Life spoke to him about the new initiative, why it’s so crucial to start now, and what he hopes they can accomplish by working together.

 Why is there a need for a coordinated effort to the study the microbiome now?

Microbiology is coming to a point where it’s becoming extraordinarily evident that bacteria, fungi and viruses play a massive role in the development of health and disease in humans and ecological ecosystems, and in regards to the ways in which we can moderate or augment those environments. We’re starting to find that we have a unique ability—through the microbiome—to control how environments work, and maybe even use the bacteria as a method of tracking those environmental changes. So we’re at a point now where if we coordinate our activities as a community, we can go after the really big questions. But coordinating a community that is so diverse and so disciplined actually requires identifying and targeting the fundamental questions which underpin microbial ecology, and microbial interactions across the board, from oceans and soils, to plants and animals and humans, to built environments.

We need to be able to work on the fundamental scientific questions across the entire system, to really develop that understanding of fundamental science. This is essentially what physicists grabbed ahold of 30-50 years ago. They came together as a community and started to understand those fundamental principles, and then identify the biggest questions each year and utilize that as a galvanizing element for the community to ask the funding agencies and the commercial companies to fund this research. We are hijacking that model, and coming together as a community with private donors, foundations, federal agencies and commercial entities to develop the funding mechanism to begin answering the fundamental questions that underpin microbiology in all contexts relevant to human health and environmental science.

All of the institutions involved in this initiative have been doing their own microbiome research already. What’s the benefit of working together?

The benefit of doing it together is pooling expertise and resources to address specific aspects of particular scientific questions. So for example, if I want to understand the fundamental principles that govern how bacteria communicate in any setting, whether it’s in the gut or your mouth or the ocean or the soil, I need to have people who are experts in protein folding and biology at the molecular level. I also need to have people who are gifted in exploring bacterial cell systems biology and community systems biology and metabolic dynamic interactions. I need physicists and engineers to design and build the platform technologies to help us look at microbes at that level. We also need researchers from many different disciplines to analyze that data and compute it on a large scale, so that we can create models of how bacteria communicate, and then apply those models to all of the different contexts in which the microbes find themselves.

So if you will, we want to build CERN (the European Organization for Nuclear Research) for microbiology. But we can’t build CERN—there isn’t one big tool like a particle accelerator that will help us answer our questions. We need to unify ourselves across the different disciplines to create institutional collaborations that bridge disciplinary boundaries to integrate our research objectives towards a common goal. We can do that in small cohorts at the moment, but we really don’t have the infrastructure to allow some of the larger groups of individuals to come together under a single umbrella.

The Human Microbiome Project did this reasonably well. It brought the medical community and the environmental sciences community together under a single umbrella. It was a $180 million program, but it wasn’t big enough; and it was very focused on one specific research theme, the human microbiome. Well, we learned a lot from that study. We want to raise $500 million and bring together researchers to answer fundamentally different questions. We need to bring together researchers from different universities, national labs and commercial organizations to really address the gaps in data infrastructure, computational tools, engineering tools, cell manipulation, protein characterization and identification, molecular microbiology tools and ecological analyses. We have so many gaps in our ability right now. If we came together as a community, we could really start to plug those gaps systematically in order to build a brighter future.

Bacteria from the human mouth (Credit: Jessica Mark Welch, Marine Biological Laboratory)

Bacteria from the human mouth (Credit: Jessica Mark Welch, Marine Biological Laboratory)

How will this group be organized? How will it work in practice?

In practice, we would envision having an oversight board and a governance board that would explore how funding resources made available through federal agencies, private foundations, and commercial entities—whether they are in-kind or technological development or funding—how those resources should be available to the community.

You can’t rely on one federal organization to deliver a cogent strategy across disciplines that fall outside of their mandate. For example, the Department of Energy shouldn’t focus on funding research into the interactions between cancer and microbial communities in humans. What we need is an oversight committee that actually enables that. We also don’t want to just have one group working with one industrial partner being funded by one foundation. We want dozens of universities and national labs coming together, where each community is explicitly designed to perform an operation relevant for the particular research question. Then we can identify the industrial partnerships which can support and benefit from the science ongoing in that partnership, and then identify the resources—be they a combination of private foundations and federal agencies—which can contribute funds to the development of that scientific case in a way that’s cogent and reduces the administrative boundaries.

It sounds like heaven, but it needs to be done. If we don’t do this, we are seriously limiting the ability of this community to deliver science at a level that is advantageous for humanity.

What are the next steps for the initiative?

We’ve finished multiple rounds of discussions, and we are now bringing together the relevant foundations, federal agencies and industrial partners who can benefit from being involved with this kind of operation. That in and of itself is probably going to take the next year to coordinate. Hopefully sometime in 2017, we will start to explore specific funding calls out to address particular areas identified by the community for scientific investigation.

As a community, we will put together these large-scale consortia focused on a particular area of research, and then we will work with an oversight committee to implement a funding strategy that is appropriate over the next decade. We are working with the White House Office of Science and Technology Policy, and we hope to model the United Microbiome Initiative after the BRAIN Initiative that was launched in 2013.

What’s the end goal? What do you hope to see in 2027 after a Unified Microbiome Initiative has been running for 10 years?

My hope is that in the next 10-15 years, we will develop a series of consortia that really help to streamline the process of developing fundamental science, and streamlining the application of that science to real world problems. Today that is being done in a piecemeal fashion. We have research projects, and they create potential intellectual property that is then drip-fed through to a very small number of companies. It really reduces the translational impact of any research, whether that’s creating the next generation of biofuels, creating novel therapeutics or developing remediation technologies for cleaning up waste. Whatever it is, we need to be able to streamline the translation of that basic research into these practical outcomes. That is going to be the gold standard end goal.

We should be working as a community to leverage the best attributes of every research community to create this. We need the relevant expertise for each component of this process, from basic research all the way up to translation and disseminating commercial products. We need everybody working together, and to do that we need an infrastructure that supports the funding, the R&D, and the implementation of it. Without it we’re going to struggle, when we could be taking leaps and bounds ahead in our understanding of the microbiome.

About Matt Wood (531 Articles)
Matt Wood is a senior science writer and manager of communications at the University of Chicago Medicine & Biological Sciences Division.
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