Throwing a New Light on Microbial Dark Matter

May 13, 2016

It is always a special moment—a signal that something major is about to happen—when the science advisor to the President of the United States calls 100+ scientific leaders to the White House for an announcement. For ASM leadership, the announcement on Friday, May 13, of a new national initiative to accelerate discoveries in microbiome research was particularly exciting. ASM was front-and-center for the event because we are front-and-center in this exploding research area.

The path to great discoveries is rarely linear, but instead follows a convoluted tangle of paths with many dead ends and sudden connections from seemingly irrelevant directions. If science research were a cookbook, its spattered pages would list as ingredients intuition, pure curiosity, hypothesis testing, serendipity, perseverance and luck (both good and bad). This cookbook of phenomenal discoveries would have many chapters describing how new technologies can add new flavors and new dishes to the banquet of research and innovation.

For example, much of what’s cooking in today’s laboratories comes from our new capabilities in sequencing the human genome. “Next generation sequencing” has revolutionized genetics and molecular research in labs around the world. Another technological giant step, super-resolution microscopy, has transformed cell biology by giving researchers the ability to observe and understand living cells at a molecular level without relying on static images of defunct cells. The list of new methods certainly goes on but I would add one more, metagenomics. At this very moment, metagenomics is reinventing the microbial sciences, enabling the detection of the vast majority of microorganisms which previously could not be cultured nor otherwise identified. Metagenomics is at the core of the microbial sciences renaissance we are observing today. This is not just another neat tool for research biologists but represents the promise of a major advance for humanity, since microbes affect the most daunting problems we face. To name just a few hot button issues, microbes are central to emerging and reemerging infectious diseases, alternative energy sources, environmental stewardship and climate change.

This was the scientific back story behind the unveiling last Friday, May 13, of the National Microbiome Initiative (NMI) by John Holdren, the Senior Advisor to the President on Science and Technology. For myself and the many other ASM members present, it was an electrifying moment. As CEO of ASM, I found myself surrounded by leaders from all the microbial sciences, together with executives and program officers from all the chief public and private funding agencies. I saw familiar faces and familiar name tags from the Department of Energy, the National Science Foundation, the Department of Agriculture and the National Air and Space Agency along with leaders from noted philanthropic organizations. We were all there to give microbiome research a head start toward meeting the challenges of the mid-21st century on Earth.

The NMI will concentrate on finding ways to ease significant bottlenecks currently slowing the development of microbiome understanding. Ordinarily, I am a staunch supporter of investigator-initiated research and, as such, not typically a big fan of big initiatives. Many times these big initiatives never overcome their “top-down” origins but with the NMI, it is clear to me that microbiome requires a coordinated approach, rooted in many smaller projects. In fact, significantly different areas of research need to come together and the research community needs incentives and special opportunities to draw together radically different approaches, skills, and thought processes, which under current conditions would be unlikely to happen organically. This is the collective spirit that I see driving the microbiome initiative, and therefore it is more than welcome.

So on Friday, I was bursting with pride because ASM is front-and-center in this initiative, especially when it was announced that The Kavli Foundation is donating $1 million to a consortium led by ASM including the American Chemical Society (ACS) and the American Physical Society (APS) to launch the Kavli Microbiome Ideas Challenge grant program. The goal is to fund bold ideas in basic science to circumvent current technological obstacles hindering microbiome research. It was truly exciting to imagine how The Kavli Foundation grant will bring together so many diverse fields from chemistry to physics to material sciences in order to tackle tomorrow’s most daunting problems. After the White House event, ASM hosted a reception at its Dupont Circle headquarters and the room buzzed loudly with a common excitement.

At ASM, we didn’t party long. Already we’ve issued a proposed roadmap for microbiome research through an editorial in the ASM journal mBio, entitled “Toward a Predictive Understanding of Earth’s Microbiomes to Address 21st Century Challenges.” It should be required reading for everyone in our science. The editorial makes clear the impact that microbes have on our biosphere and its noisiest inhabitants, humans. The authors, including ASM Past President Tim Donohue, focus on the challenges that society and our planet face and how directly they are affected by microbial activities. The editorial highlights six areas:

  • The role of microbes in the formation of our biosphere.
  • Global challenges of human population growth and environmental change.
  • The role of microbiome research to improve human health and resilience.
  • Urbanization and the intersection of human and environmental microbiomes.
  • The societal benefits from harnessing microbiome functions.
  • Understanding what the authors call, “Microbial Dark Matter,” a clever analogy that underscores how little we really know about the stupendous diversity of the global microbial community.
The authors identify current roadblocks and what we need to breach them, moving microbiome research further and faster. They cite the need for:
  • Decoding functions of microbial genomes.
  • Characterizing the physical and chemical structure of microbial habitats.
  • Developing better technologies for robust, portable, genome-centric analyses of microbiomes.
  • Building the framework for massively parallel, genome-centric quantitative microbiome analysis.
  • Developing and integrating tools for robust hypothesis testing.

‚ÄčThis is just the beginning. The National Microbiome Initiative is only the first light to be thrown by these new technologies on the dark matter that undergirds life on earth. We hope that the NMI will quickly make the microbiome a little less dark for scientists and the public. While we can’t predict the path of great discovery, we believe that the NMI could be a beacon for microbiologists and our new scientific and technological allies as we press ahead toward leveraging the boundless power of microbes to improve health, the environment, food security and energy sustainability. We did a little celebrating at ASM on Friday, but everyone there knew that on Monday we had lot of work ahead of us.

Author: Stefano Bertuzzi

Stefano Bertuzzi
Stefano Bertuzzi is the CEO of the American Society for Microbiology.