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White House Announces $121 Million Federal Investment in National Microbiome Initiative
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The White House Office of Science and Technology Policy today announced the National Microbiome Initiative, which aims to advance understanding of microbiomes across different ecosystems, and enable protection and restoration of healthy microbiome function.
In addition, more than 100 non-government groups have responded to the OSTP’s national call to action in January by committing more than $400 million to support microbiome research.
Adding to ongoing federal investments in microbiome research, the NMI will launch with more than $121 million in total federal investments in the 2016 and 2017 fiscal years, including investments from the Department of Energy, NASA, NIH, the National Science Foundation and the U.S. Department of Agriculture.
NMI goals
The NMI was revealed today at an event hosted by the OSTP that brought together federal agencies and private-sector stakeholders who will contribute to the advancement of the initiative.
“The goals of the initiative are to address fundamental questions that span multiple microbiomes, develop platform technologies for studying many microbiomes, and then develop a workforce that can do this job and also ... expand our current workforce to tackle more and different environments than we can study with just the regular scientific community,” Jo Handelsman, PhD, associate director for science at the White House OSTP, said during the National Microbiome Event.
These three key areas of focus for the NMI were the result of a year-long collaboration of federal, academic and private sector scientists from many different fields, who collectively evaluated the scope of federally funded microbiome research to identify knowledge gaps and guide future efforts. Bringing experts from different scientific fields together — from microbiologists to physicists, technologists and computer scientists — are essential to microbiome research and the goals of the NMI, Handelsman said. “It’s going to be these interdisciplinary discussions that will probably lead to the big innovations and creative solutions.”
The tools that will be developed by the NMI have “huge implications,” not only in the “basic understanding of how bacteria interact, but also in how we approach medicine as a whole,” according to Congresswoman Louise M. Slaughter (D-New York). “What’s happening here is really pushing all the boundaries ... The idea of learning what [the microbiome’s] purpose is, is so critical, it’s going to be like splitting the atom,” she said during the event. In particular, this research could help improve food safety, and the development of precision antibiotics could help to fight the continuing antibiotic resistance problem, she added.
Building on Federal Microbiome Research
The NMI builds on years of federal microbiome research efforts, involving more than a dozen federal departments and agencies. However, investment in this research has recently grown, tripling between fiscal years 2012 and 2014 with a total of $922 million in investments from these departments.
During the 2012-2014 fiscal years, NIH has invested $491 million into microbiome-related research for diabetes, obesity, cardiovascular disease, autism, asthma, cancer, preterm birth, brain development and behavior. Notably, the NIH also launched the Common Fund’s Human Microbiome Project in 2008 to develop foundational research resources to catalyze the field of microbiome science.
“We’ve invested more than $215 million in it to date, and it has served that catalytic purpose very nicely,” David M. Murray, PhD, associate director for prevention at NIH, said during the event.
NIH funding for microbiome research quadrupled to $23 million the year the Human Microbiome Project began, and increased 10-fold during the next decade, “with a fraction of that coming from the Human Microbiome Project and most of it coming from the other institutes and centers at NIH,” he said. “So this catalytic function of the Common Fund Project has worked out very nicely; it got started with the Human Microbiome Project, it has spread like wildfire, and microbiome research is now flourishing across the campus at NIH.”
NIH investigators are currently studying the biology of the microbiome in terms of microbial function and activities, as well as host-microbe interactions, Murray added. “Future studies are going to require collaborations among biologists, data scientists, ecologists, modelers and others who will advance our understanding of this host–microbe interaction and their influence on health and disease, because that after all is what NIH is most interested in.”
More than $230 million in microbiome research across NIH is expected in fiscal year 2016, with at least $20 million focused on foundational questions and tools development, and a similar level of support is expected in fiscal year 2017, he said.
Support From Non-Government Institutions
In addition to new federal funding, it was announced at the event that more than 100 external institutions have committed more than $400 million in financial and in-kind contributions to support microbiome research and the NMI goals.
These include the Bill and Melinda Gates Foundation, which will invest $100 million in developing human and agricultural microbiomes research tools over 4 years. In particular, this investment will support clinical studies evaluating the effects of the human microbiome on childhood malnutrition and stunting, and projects examining how soil microbiomes can be used to mitigate crop pests and diseases in sub-Saharan Africa.
Other institutions have made commitments to support interdisciplinary microbiome research, including the Ann Romney Center for Neurologic Disease at Brigham and Women’s Hospital, which will establish a multidisciplinary center to study the microbiome and neurological and related immune diseases; Evelo Biosciences, which will provide $1 million in grants for studies of the human microbiome and cancer; and the University of Chicago, which is investing $1.3 million to launch The Microbiome Center to study the microbiomes across ecosystems.
Others have committed to developing platform technologies to enable novel approaches for research. For example, Vedanta Biosciences will invest $40 million during the next 2 years to advance translational microbiome research, the Mayo Clinic Center for Individualized Medicine will open a new $1.4 million Microbiome Clinic offering new clinical services, diagnostics and education, and Metabiomics will invest $23.5 million to develop a noninvasive test for detection of colorectal cancer and polyps using microbiome biomarkers.
Finally, many institutions will also contribute resources to expand the microbiome workforce. The AGA has committed to investing $100,000 to support early-career investigators and will host its first health care professionals meeting, the American Gut Project plans to expand its partnerships to improve understanding of the human microbiome, and Dannon will partner with AGA to increase fellowship support and provide a $20,000 Gut Microbiome Health Award for microbiome research.
Just the Beginning
The NMI represents “only the beginning” of the microbiome research effort, according to John P. Holdren, PhD, Assistant to the President for Science and Technology and Director of the OSTP.
“Today’s cutting edge research and the technical advances that translate research in to application … have so far only provided us a glimpse of the promise that advanced understanding of how communities of microbes behave will ultimately hold,” he said. “Such insights have the potential to yield advances with lasting benefits for human plant and animal health, for agriculture, for renewable energy production, for water treatment, for environmental remediation and more.”
Holdren also echoed the importance of interdisciplinary collaboration in future microbiome research efforts, as emphasized in the three core goals of the NMI.
“Achieving that vision will require new strategies for collaborative research across multiple microbiome ecosystems, it’ll require new tools to generate insights and translate knowledge, and maybe most importantly, it will require investments in a skilled and dedicated microbiome workforce to drive discovery forward.”
The microbiome initiative, like many other efforts led by this administration, is an “all hands on deck” effort, he concluded. – by Adam Leitenberger
Perspective
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Gregg J. Silverman, MD
In recent years, an entirely new perspective has developed on how the microbes present on and in our bodies directly impact diverse facets of health, immune defenses and susceptibility to disease. The highest density of commensal bacteria in the human intestine, which carries a vast and diverse microbial ecosystem of 1,013 to 1,014 bacterial cells, can be from 35,000 different types of bacteria that live within the body. These bacteria have co-evolved with our species and are essential for human health.
From this perspective, we each possess an “extended genome” of millions of microbial genes located in the intestine, which is 100-fold larger than the human host, encompassing hundreds of species. This multigenomic symbiosis is expressed at the proteomic and metabolic levels in the host. In particular, we need our microbiome as these bacteria are essential to digest food and provide essential vitamins and nutrients. Some of the bacteria modulate the innate and adaptive immune systems and help boost immune defenses from truly pathogenic microbes and viruses.
Imbalances in our microbiomes can lead to imbalances in the distribution among the multitude of different species. For example, if one has inherited genes that make one predisposed to a disease, then bacterial imbalances may trigger medical conditions that otherwise may not have developed.
In hospitalized patients who receive broad spectrum antibiotics, when the bacterial suppressors wear off, the bacterial populations in the bowel can be overgrown by Clostridium difficile that makes a toxin that can cause a life-threatening damage to the bowel called pseudomembranous colitis. In the past, we had no choice but to subject affected patients to more rounds of antibiotics with the hope of re-establishing a healthy balance. However, this is not always successful and better treatments are needed. We need to better understand what represents a healthy balance and how we can re-establish it when lost.
In rheumatology, there is mounting evidence that there are individuals in which expansions of a bacterial commensal called Prevotella copri can trigger rheumatoid arthritis. Researchers are looking for similar links with psoriasis and psoriatic arthritis.
The call from the White House seeks to bring greater attention to the need to understand how the microbiome influences health. Recent advances from Next Generation Sequence has allowed researchers to efficiently survey the abundance of different bacteria in a sample based on using technology to efficiently catalogue bacteria based on their genes. DNA sequences, the most essential blueprints of life, help us understand how we can improve health and perhaps treat challenging diseases.
Hopefully, the federal investment will attract researchers from other fields with new ideas to help scientists develop better instruments and technologies needed for advanced investigations. The increase in funds will go to many different research institutes, medical schools and hospitals, for the support of research teams to work to cure disease, avoid the start of microbiome medical conditions and help patients live longer and better.
References:
Bengmark S. Gut. 1998;42(1):2-7.
Gill SR, et al. Science. 2006;2;312(5778):1355-1359.
Scher JU, et al. Nat Rev Rheumatol. 2011;doi:10.1038/nrrheum.2011.121.
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