Microbiomes could hold keys to improving life as we know it
Date: Oct 28, 2015
A Unified Microbiome Initiative to accelerate microbiome research would unlock new insights and speed translation of discoveries into numerous potential technologies for health, industry, and the environment
(BOSTON) — A consortium of 48 scientists from 50 institutions in the United States — including Pamela Silver, Ph.D., a Core Faculty member at the Wyss Institute for Biologically Inspired Engineering at Harvard University — are calling for a Unified Microbiome Initiative that would span national cross-institutional and cross-governmental agency support. The group, called the Unified Microbiome Initiative Consortium (UMIC), envisions that a coordinated effort would drive forward cutting edge microbiome research, enabling breakthrough advances across medicine, ecosystem management, sustainable energy and production of commodities. Their proposal was published online in the journal Science on October 28.
Microbial life forms including viruses, bacteria and fungi are the most diverse and abundant organisms on earth. They have shaped our evolutionary origins for billions of years and continue to have widespread impact on the planet, its environment and the species inhabiting it. Together, they make up microbiomes that influence each other, the environment, and the host organisms that these microbial communities thrive in. The UMIC foresees that the microbiomes populating our planet and its many diverse species and environments could be leveraged through genetic engineering for applications that improve the greater good, and that many milestones could be reached on this front within ten years.
Credit: Wyss Institute at Harvard University
"Microbes are everywhere. Therefore understanding microbiomes, whether they be the ones that live in and on our bodies or the ones in the environment, is essential to understanding life," said Silver, who in addition to being one of the faculty leaders on the Wyss Institute's Synthetic Biology platform, is also the Elliot T. and Onie H. Adams Professor of Biochemistry and Systems Biology at Harvard Medical School (HMS) and a founding member of the Department of Systems Biology at HMS.
The UMIC consists of leading microbiologists, ecologists, physical scientists, engineers, and scientists in the emerging field of synthetic biology. The group coalesced during a series of coordinated but separately convened meetings held by The White House Office of Science and Technology Policy and The Kavli Foundation. The proposal in Science got its roots from the UMIC's efforts to identify challenges and opportunities in microbiome research as well as their strategic recommendations for accelerating discovery that emerged from these meetings.
"Understanding how [microbiomes] work might hold the key to advances as diverse as fighting antibiotic resistance and autoimmune diseases, reclaiming ravaged farmland, reducing fertilizer and pesticide use, and converting sunlight into useful chemicals," said Jeff F. Miller, Ph.D., Director of the California NanoSystems Institute and corresponding author of the Science paper.
By metabolic processes, microbes synthesize countless different molecules, which through genetic engineering could lead to colonies of microbial "workers" being used for the sustainable synthesis of pharmaceuticals, materials and chemical commodities. Genetically engineered microbes could also produce biofuels through metabolic processes and conversion of solar energy into liquid fuel, according to work already underway by Silver at the Wyss Institute and HMS.
Microbes also play a vital role in balancing biogeochemical processes, such as removing carbon dioxide from the atmosphere. The interactions between soil, plant roots and microbes play an important role in plant health and crop yield.
Furthermore, the microbiomes in our gastrointestinal tracts regulate wide-ranging physiological, metabolic, immunologic, cognitive, behavioral, and psychiatric traits. Understanding and manipulating human microbiomes could be key to managing physical and mental health. Silver and her team have already begun developing several potential avenues for leveraging gut microbes to improve health. In collaboration with Wyss Core Faculty member James Collins, Ph.D., Silver has engineered genetically programmed bacterial "reporters" that can detect and record conditions in the gastrointestinal tract. And, working with Wyss Institute Founding Director Donald Ingber, M.D., Ph.D., and Wyss Institute Senior Staff Scientist Jeffrey Way, Ph.D., Silver is developing consortia of synthetic microbes that could be used to treat gastrointestinal illness.
Her expertise and experience in these emerging areas of synthetic biology has enabled Silver to contribute her thought leadership as a member of the UMIC to how the proposed Unified Microbiome Initiative could integrate focus areas to accelerate microbiome research.
In this animation, see an example of how genetically engineered microbes being developed by Wyss Institute Core Faculty member Pam Silver could detect and treat a wide range of gastrointestinal illnesses and conditions. Silver is one of 48 United States scientists on the Unified Microbiome Initiative Consortium, which is calling for national coordinated efforts to accelerate microbiome research in a proposal published in Science journal. Credit: Wyss Institute at Harvard University
"I'm interested in engineering microbes as a way to interrogate their behavior," said Silver. "The purpose of this unified initiative is to determine what are the big questions we have about the microbiome and what are the specific technologies we need in order to investigate those questions."
Some of the big questions the group hopes to address through an organized coalition include understanding how microbes assemble into communities and what makes them resilient or resistant to perturbation, how genes in the microbiome interact with one another, which genes in the microbiome are associated with which organisms, as well as how we can beneficially harness the microbiomes of humans, animals, plants and environments.
To find the answers to these questions, scientists must first be supported in the development of breakthrough technologies for investigating microbiomes. Specifically, the group recommends development of improved computational methods for analyzing and predicting the vast number of unknown genes and their functions comprising microbiomes; a transition from gene-specific to whole-genome based analysis through improved genome reference libraries and sequencing methods; developing high-powered imaging methods for visually interrogating communities of microbes down to the individual level; new adaptive modeling systems and data reporting tools; improved genetic engineering techniques for perturbing microbial communities; and novel methods to mimic natural environments for supporting microbiome growth in the laboratory, among others.
"Discovery of the existence and importance of the microbiome has provided a new frame of reference for our understanding of health and our environment," said Ingber, who in addition to directing the Wyss Institute is the Judah Folkman Professor of Vascular Biology at HMS and Boston Children's Hospital and Professor of Bioengineering at the Harvard John A. Paulson School of Engineering and Applied Sciences. "A nation-wide coordinated effort to invest in understanding and leveraging microbiomes could open entirely new frontiers in biotechnology and medicine, and lead to solutions that would not be possible in any other way."
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The Wyss Institute for Biologically Inspired Engineering at Harvard University (http://wyss.harvard.edu) uses Nature's design principles to develop bioinspired materials and devices that will transform medicine and create a more sustainable world. Wyss researchers are developing innovative new engineering solutions for healthcare, energy, architecture, robotics, and manufacturing that are translated into commercial products and therapies through collaborations with clinical investigators, corporate alliances, and formation of new startups. The Wyss Institute creates transformative technological breakthroughs by engaging in high risk research, and crosses disciplinary and institutional barriers, working as an alliance that includes Harvard's Schools of Medicine, Engineering, Arts & Sciences and Design, and in partnership with Beth Israel Deaconess Medical Center, Brigham and Women's Hospital, Boston Children's Hospital, Dana–Farber Cancer Institute, Massachusetts General Hospital, the University of Massachusetts Medical School, Spaulding Rehabilitation Hospital, Boston University, Tufts University, Charité – Universitätsmedizin Berlin, University of Zurich and Massachusetts Institute of Technology.
Harvard Medical School (http://hms.harvard.edu) has more than 7,500 full–time faculty working in 11 academic departments located at the School's Boston campus or in one of 47 hospital–based clinical departments at 16 Harvard–affiliated teaching hospitals and research institutes. Those affiliates include Beth Israel Deaconess Medical Center, Brigham and Women's Hospital, Cambridge Health Alliance, Boston Children's Hospital, Dana–Farber Cancer Institute, Harvard Pilgrim Health Care, Hebrew Senior Life, Joslin Diabetes Center, Judge Baker Children's Center, Massachusetts Eye and Ear Infirmary, Massachusetts General Hospital, McLean Hospital, Mount Auburn Hospital, Schepens Eye Research Institute, Spaulding Rehabilitation Hospital and VA Boston Healthcare System.