THE WHITE HOUSE. Announcing the National Microbiome Initiative




FACT SHEET: Announcing the National Microbiome Initiative

WASHINGTON, DC Today, the White House Office of Science and Technology Policy (OSTP), in collaboration with Federal agencies and private-sector stakeholders, is announcing a new National Microbiome Initiative (NMI) to foster the integrated study of microbiomes across different ecosystems, and is hosting an event to bring together stakeholders vital to advancing the NMI.

Microbiomes are the communities of microorganisms that live on or in people, plants, soil, oceans, and the atmosphere. Microbiomes maintain healthy function of these diverse ecosystems, influencing human health, climate change, food security, and other factors. Dysfunctional microbiomes are associated with issues including human chronic diseases such as obesity, diabetes, and asthma; local ecological disruptions such as the hypoxic zone in the Gulf of Mexico; and reductions in agricultural productivity. Numerous industrial processes such as biofuel production and food processing depend on healthy microbial communities. Although new technologies have enabled exciting discoveries about the importance of microbiomes, scientists still lack the knowledge and tools to manage microbiomes in a manner that prevents dysfunction or restores healthy function.

The NMI aims to advance understanding of microbiome behavior and enable protection and restoration of healthy microbiome function. In a year-long fact-finding process, scientists from Federal agencies, academia, and the private sector converged on three recommended areas of focus for microbiome science, which are now the goals of the NMI:

  1. (1)  Supporting interdisciplinary research to answer fundamental questions about microbiomes in diverse ecosystems.

  2. (2)  Developing platform technologies that will generate insights and help share knowledge of microbiomes in diverse ecosystems and enhance access to microbiome data.

  3. (3)  Expanding the microbiome workforce through citizen science, public engagement, and educational opportunities.

The NMI builds on strong and ongoing Federal investments in microbiome research, and will launch with a combined Federal agency investment of more than $121 million in Fiscal Year (FY) 2016 and 2017 funding for cross-ecosystem microbiome studies. This includes:

  •   The Department of Energy proposes $10 million in new funding in FY 2017 to support collaborative, interdisciplinary research on the microbiome.

  •   The National Aeronautics and Space Administration (NASA) proposes $12.5 million in new funding over multiple years to expand microbiome research across Earth’s ecosystems and in space.

  •   The National Institutes of Health will invest an extra $20 million into microbiome research in grants in FY 2016 and FY 2017 with a particular emphasis on multi-ecosystem comparison studies and investigation into design of new tools to explore and understand microbiomes.

  •   The National Science Foundation proposes $16 million in FY 2017 for microbiome research that spans the spectrum of ecosystems, species, and biological scales.

  •   The U.S. Department of Agriculture proposes more than $15.9 million for FY 2017 to expand computational capacities for microbiome research and human microbiome research through the Agricultural Research Service, and approximately $8 million for FY 2017 to support investigations through the National Institute of Food and Agriculture of the microbiomes of plants, livestock animals, fish, soil, air, and water as they influence food-production systems.

    In addition, following OSTP’s national call to action issued in January, more than 100 external institutions are today announcing new efforts to support microbiome science. These include:

  •   The Bill and Melinda Gates Foundation will invest $100 million over 4 years to investigate and develop tools to study human and agricultural microbiomes.

  •   JDRF will invest $10 million over 5 years to address microbiome research related to type 1 diabetes.

  •   The University of California, San Diego, is investing $12 million in The Center for Microbiome Innovation to enable technology developers to connect with end users.

  •   One Codex is launching a public portal for microbiome data, allowing greater access to this data for researchers, clinicians, and other health professionals.

  •   The BioCollective, LLC, along with the Health Ministries Network, are investing $250,000 towards building a microbiome data and sample bank, and the engagement of underrepresented groups in microbiome research.

  •   The University of Michigan, with support from the Howard Hughes Medical Institute and Procter and Gamble, will invest $3.5 million in the Michigan Microbiome Project to provide new research experiences for undergraduate students.

  • Federal Involvement in Microbiome Research to Date

The Federal Government has been investing in microbiome for many years. More than a dozen Federal departments and agencies support microbiome research today, and the magnitude of investment has recently grown: a 2015 report released by the National Science and Technology Council (NSTC) noted that annual Federal investment into microbiome research tripled over FY 20122014, with more than $922 million invested during this 3-year period. This figure includes multi-agency collaborations and independently funded work. Notable Federal investments and accomplishments in microbiome research to date include:

  •   In 2007, the Department of Energy (DOE) and the National Institutes of Health (NIH) together launched the open-source bioinformatics pipeline MG-RAST (Metagenomics Rapid Annotations using Subsystems Technology), an open-source web application server that provides quantitative information on microbial populations. MG-RAST now has over 12,000 registered users and nearly a quarter million data sets.

  •   The Department of Justice (DOJ), National Institute of Justice (NIJ) invested $3.2 million in FY 2015 in microbiome related research. NIJ is the leading agency in funding forensic science research and has focused its microbiome portfolio on: the necrobiome as an indicator of time-since-death in the investigation of human remains, the soil microbiome for analysis of trace soil evidence, and the trace microbiome as an orthogonal method to human DNA analysis for associating people with evidence and environments.

  •   In FY 2016, the Department of Veterans Affairs (VA), Office of Research and Development (ORD) is investing $4.2 million in microbiome research efforts. This research spans a spectrum of diseases and medical conditions, including investigating the role of the microbiome in alcoholic liver disease and cirrhosis, characterizing components of the nasal microbiome that could prevent transmission of methicillin-resistant Staphylococcus Aureus (MRSA) in VA hospitals, and determining the role of the microbiome in preventing or reducing infection at the implant sites of Veterans receiving certain prosthetic lower limb implants. These research efforts aim to enhance the well-being and health of American Veterans, as well as contribute to the broader research fields surrounding microbiome related disciplines, studies, and treatments.

  •   In FY 2007, NIH initiated the 10-year Human Microbiome Project (HMP) to develop foundational research resources to catalyze the field of microbiome science. Roughly 50,000 files of sequence and other genomic data from HMP is now publicly available through repositories such as GenBank, Sequence Read Archive (SRA), and the Genotype and Phenotype database (dbGaP), and this past year, approximately 75,000 users from 178 countries accessed HMP data. A total of $215 million has been invested in the HMP since its inception, with $50 million of that total invested over FY 2012-2014.

  •   Over FY 2012-2014, NIH invested $491 million into research that explores the involvement of the human microbiome in conditions as diverse as diabetes, obesity, cardiovascular disease, autism, asthma, cancer, preterm birth, brain development, and behavior. This funding was distributed across 19 of the 27 NIH Institutes and Centers, and was expended mostly through grants to individual university investigators and for intramural research support.

  •   The National Institutes of Standards and Technology (NIST), in collaboration with NIH, has organized the Standards for Microbiome Measurements workshop for later this year. The workshop will bring together stakeholders from other Federal agencies, academia, and industry to identify priorities for and plan the creation of reference materials, protocols, and measurement tools that will accelerate development of microbiome-based clinical treatments and marketable products.

  •   In FY 2016, the National Oceanic and Atmospheric Administration (NOAA) Oceanic & Atmospheric Research (OAR) line office begins an initiative to support microbiome research efforts at a level of $1.8 million. The multi-pronged effort includes close collaboration with NOAA's National Marine Fisheries Service (NMFS) line office, the J. Craig Venter Institute (JCVI), the Monterey Bay Aquarium Research Institution, and academic partners, including the Scripps Institute of Oceanography and the University of Miami. NOAA’s projects include microbiome metagenomic and metatransciptomic work to support ecosystem understanding and fisheries assessment, microbiome assessment via in-situ and mobile technologies, and metagenomics research to garner intelligence on higher trophic levels via ocean microbiome assessment.

  •   The National Science Foundation (NSF) and the Department of Agriculture (USDA) supported the Joint Microbial Genome Sequencing Program for 10 years, starting in FY 2000. The program provided genetic sequences of hundreds of ecologically relevant and agriculturally important bacteria, viruses, fungi, and oomycetes (water molds). NIH, NSF and the USDA National Institute of Food and Agriculture (NIFA) are currently supporting the Joint Ecology of Infectious Diseases Program. Both programs encourage timely and broad data sharing through the use of public repositories.

  •   The Smithsonian Marine Station (SMS) has invested in two microbiome projects in FY 2016, which include $50,000 to work with collaborators across the United States to understand the roles that microorganisms play in healthy coral reef ecosystems. Additionally, the Smithsonian Marine Station has invested $120,000 on understanding healthy and diseased coral microbiomes.

USDA Agriculture Research Service (ARS) invested $11.9 million in FY 2015 in microbiome research. The investments included animal-microbiome research that encompassed alternatives to antibiotics to enhance feed efficiency; plant-microbiome research to learn how crop productivity and quality can be influenced; soil- microbiome research that optimizes the nutrient cycle and prevents soil degradation and enhances sustainability; and human-microbiome research, which focuses on the gut microbiome in immune-system development and its effect on disease resistance, health, and well-being.

In addition, the newly chartered NSTC Microbiome Interagency Working Group (MIWG), will develop a Federal Strategic Plan for microbiome research. The Plan will outline an approach for addressing research needs and gaps identified in the November 2015 Report of the Fast-Track Action Committee on Mapping the Microbiome, and recommend ways to improve coordination of microbiome research among Federal agencies.

The NMI will build on these past and ongoing activities by supporting more interagency cooperation and interdisciplinary and cross-ecosystem research to enable the next breakthrough discoveries in microbiome science.

Federal Investments in Support of the National Microbiome Initiative

The NMI will launch with more than $121 million of strategic investments from Federal agencies into interdisciplinary, multi-ecosystem microbiome research and tools development. This investment is based on funds appropriated in FY 2016 and proposed in the President’s FY 2017 Budget.

  •   The DOE Office of Science proposes $10 million in new funding in FY 2017 to support collaborative, interdisciplinary research on the microbiome. Research will focus on both experimental systems and new computational tools to generate predictive models of microbiomes. Priorities for funding will include partnerships among DOE national labs, academia, and field research facilities (such as those supported by USDA) and projects in mission-relevant environments such as biomass-focused agricultural systems and terrestrial ecosystems vulnerable to climate change.

  •   The National Aeronautics and Space Administration (NASA) proposes $12.5 million in new funding over multiple years to expand microbiome research across Earth’s ecosystems and in space. This includes $2.5 million for the Human Exploration Research Analog (HERA) study, scheduled to begin in January 2017. NASA is also investing $10 million in FY 2016 funding in the Ocean Worlds program, to support development life-detection technologies to search for microbiomes on other planetary bodies in our solar system.

  •   In addition to its normal review and support of microbiome-related applications, NIH will invest an extra $20 million in grants in FY 2016 and FY 2017 with a particular emphasis on multi-ecosystem comparison studies and investigation into design of new tools to explore and understand microbiomes. The microbiome sequence and other genomic data produced in these projects will be deposited in publicly available NIH repositories or other appropriate public repositories.

  •   In FY 2017, NIST is devoting $1 million to improve the reliability and reproducibility of microbiome measurements, and engineer and model microbial ecosystems in vitro. This investment will support development of microbiome standards and reference materials, and of in vitro tools that allow complex microbial communities to be reproducibly engineered, measured, and modeled. Such resources will facilitate the translation of microbiome discoveries into useful applications in precision medicine, agriculture, and the environment.

  •   The NSF Biological Sciences Directorate (BIO) proposes $16 million in FY 2017 for microbiome research that spans the spectrum of ecosystems, species, and biological scales. This funding will be directed at interactions between microbes in the microbiomes (the inter-microbiome relationships), and also among the microbiomes of biological hosts. These studies will advance discovery of fundamental principles and research tools that transcend habitats.

  •   The NSF-NIFA Plant Biotic Interactions Program (PBI) includes $8.5 million in FY 2017 funding from NSF, and $6 million in FY 2016 funding from NIFA, for a joint agency funding of $14.5 million for proposals reviewed in FY 2016. PBI supports research on processes that mediate beneficial and antagonistic interactions between plants and their viral, bacterial, oomycete, fungal, plant, and invertebrate symbionts, pathogens, and pests. This joint NSF-NIFA program supports projects focused in current and emerging model and non-model systems and agriculturally relevant plants.

  •   USDA-ARS continues to invest substantially in animal, plant, soil, and human microbiome research efforts, with an estimated total investment of $16.9 million by the end of FY 2016. USDA-ARS has proposed over $15.9 million for FY 2017 to expand computational capacities for microbiome research and human microbiome research. This includes the development of SCINet, a new high-speed, high-capacity research network to support computationally intensive analyses of plant, animal, and soil microbiome DNA sequence data at USDA-ARS. In addition, ARS and DOE scientists are working together to develop KBase, an open platform for comparative genome analysis for agriculturally relevant plants and microbes. And on the human side, ARS will use a computer-controlled artificial intestine to study the effects of foods and their isolated constituents on the microbiomes and the metabolites produced by the bacteria.

  •   USDA-NIFA has proposed to invest approximately $8 million in new funding in the FY 2017 budget to support investigations of the microbiomes of plants, livestock animals, fish, soil, air, and water as they influence food production systems. The agency will also support studies on the role of the microbiome in the occurrence and management of antimicrobial resistance from farm to table, and the impact of climate on the microbiomes in agricultural production systems.

  •   Earlier this year, USDA-NIFA and NSF BIO established a joint funding opportunity, with $3 million from each agency (for a total of $6 million) to support the development of transformative plant and animal phenomics and microbiome technologies.

  •   The Smithsonian Institution has proposed $300,000 in new funding in FY 2017 to develop a program that will enhance its microbial research on ecosystems across the planet. The program will investigate how microbes shape ecosystem functions, services, and restoration across habitats in the United States and around the world.

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