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https://www.genome.gov/26524200/2007-release-nih-launches-human-microbiome-project

pt 1

Bethesda, Md., Wed., Dec. 19, 2007 – The human body contains trillions of microorganisms, living together with human cells, usually in harmony. Because of their small size, however, microorganisms make up only about one to two percent of the body's mass. Many microbes maintain our health, while others cause illness. Yet, surprisingly little is known about the role this astounding assortment of bacteria, fungi and other microbes play in human health and disease. To better understand these interactions, the National Institutes of Health (NIH) today announced the official launch of the Human Microbiome Project. The human microbiome is the collective genomes of all microorganisms present in or on the human body.

"The human microbiome is largely unexplored," said NIH Director Elias A. Zerhouni, M.D. "It is essential that we understand how microorganisms interact with the human body to affect health and disease. This project has the potential to transform the ways we understand human health and prevent, diagnose and treat a wide range of conditions."

Part of the NIH's Roadmap for Medical Research, the Human Microbiome Project will award a total of $115 million to researchers over the next five years. Initially, researchers will sequence 600 microbial genomes, completing a collection that will total some 1,000 microbial genomes and providing a resource for investigators interested in exploring the human microbiome. Other microbial genomes are being contributed to the collection by individual NIH institutes and internationally funded projects. A meeting between international partners was recently convened to discuss forming an international consortium.

Researchers will then use new, comprehensive laboratory technologies to characterize the microbial communities present in samples taken from healthy human volunteers, even for microbes that cannot be grown in the laboratory. The samples will be collected from five body regions known to be inhabited by microbial communities: the digestive tract, the mouth, the skin, the nose, and the female urogenital tract. Demonstration projects will subsequently be funded to sample the microbiomes from volunteers with specific diseases. This will allow researchers to correlate the relationship between changes in a microbiome present at a particular body site to a specific illness.

"We now understand that there are more microbial cells than human cells in the human body. The Human Microbiome Project offers an opportunity to transform our understanding of the relationships between microbes and humans in health and disease," said Dr. Alan Krensky, the director of the Office of Portfolio Analysis and Strategic Initiatives (OPASI), which oversees the NIH Roadmap for Medical Research.

While the term "microbiome" may be relatively new in biomedical research, most people are familiar with some of the effects - both good and bad - that microbes can have on our health. Consider the example of the biggest reservoir of microbes in humans: the digestive tract. The human gut harbors many beneficial microorganisms, including certain bacteria called probiotics. There is evidence these probiotics, found in dietary supplements, yogurt and other dairy products as well as various soy products, can stimulate the immune system and improve digestive functions. In contrast, previous research suggests that variations in the composition of microbial communities may contribute to chronic health conditions, including diabetes, asthma, obesity and digestive disorders.

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"Microbes play a significant role in the health of the digestive tract and many digestive diseases result when the microbial environment is out of balance," said Griffin P. Rodgers, M.D., M.A.C.P., director of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), and co-chair of the Human Microbiome Project's Implementation Group. "The Human Microbiome Project will help us better understand the microbial environment in the gut, as well as provide us with the tools and technology to expand our exploration into this field of research."

Traditionally, microbiology has focused on the study of individual species as isolated units, making it difficult to develop and inventory all of the microbes in and on the human body. Because their growth is dependent upon a specific natural environment, it's difficult to recreate microbe-host interactions in the laboratory. Advances in next generation DNA sequencing technologies relying on a process called metagenomic sequencing will be used. Instead of isolating each microbe, all of the DNA within the collected samples will be sequenced.

"Our goal is to discover what microbial communities exist in different parts of the human body and to explore how these communities change in the presence of health or disease," said National Human Genome Research Institute Director, Francis S. Collins, M.D., Ph.D., co-chair of the Human Microbiome Project Implementation Group. "In addition, we will likely identify novel genes and functional elements in microbial genomes that will reshape the way we think about and approach human biology."

NIH recently awarded $8.2 million to four sequencing centers, to start building a framework and data resources for the Human Microbiome Project. One-year awards were given to the sequencing centers at the Baylor College of Medicine, Houston, and Washington University School of Medicine, St. Louis, which are part of the NHGRI Large-Scale Sequencing Research Network; and the Broad Institute of MIT/ Harvard, Cambridge, Mass., and the J. Craig Venter Institute, Rockville, Md., which are funded through the National Institute of Allergy and Infectious Diseases (NIAID) Microbial Genome Sequencing Centers Program.

The objectives of this initial work are to sequence the genomes of 200 microbes that have been isolated from the human body as part of the 1,000 microbial genomes collection. Researchers will also begin recruiting healthy volunteers who will donate samples from the five body regions. NHGRI, NIAID, and the National Institute of Dental and Craniofacial Research (NIDCR) have led the initial phases of the project.

"The recent emergence of faster and cost-effective sequencing technologies promises to provide an unprecedented amount of information about these microbial communities, which in turn will bolster the development and refinement of analytical tools and strategies," saidNIAID Director Anthony S. Fauci, M.D., co-chair of theHuman Microbiome Project's Implementation Group.

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Following the precedents set by other large-scale genomics efforts, such as the Human Genome Project and the International HapMap Project, data from the Human Microbiome Project will be swiftly deposited in public databases, including those supported by the National Center for Biotechnology Information (www.ncbi.nlm.nih.gov/mapview), part of the National Library of Medicine. The project also will fund the establishment of a Data Analysis and Coordinating Center, which will coordinate data access and develop data retrieval tools for the research community.

Also following on the lead of those efforts, the Human Microbiome Project will monitor and support research on the ethical, legal and social implications of the research. Areas of focus include the clinical and health implications of using probiotics, potential forensic uses of microbiome profiles, bioterrorism and biodefense applications, the application of new technologies from the project, and patenting and privacy issues.

"Examining and addressing the emerging ethical, legal and social implications of metagenomics research is central to our goal of one day moving any resulting diagnostic, prevention, or treatment tools into the clinic in a safe and effective manner," said NIDCR Director Lawrence Tabak, D.D.S., Ph.D., co-chair for the NIH Human Microbiome Project Implementation Group.

Additional information about the Human Microbiome Project is available at www.nihroadmap.nih.gov/hmp. For more information about funding opportunities, go to: www.nihroadmap.nih.gov/hmp/grants.asp. A high resolution image of the bacteria, Entercoccus faecalis, a microbe that lives in the human gut, is available in color at www.genome.gov/dmd/img.cfm?node=Photos/Microorganisms&id=79092, or in black and white at www.genome.gov/dmd/img.cfm?node=Photos/Microorganisms&id=79093.

The Human Microbiome Project is part of the NIH Roadmap for Medical Research. The Roadmap is a series of initiatives designed to pursue major opportunities and gaps in biomedical research that no single NIH institute could tackle alone, but which the agency as a whole can address to make the biggest impact possible on the progress of medical research. Additional information about the NIH Roadmap can be found at www.nihroadmap.nih.gov.

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https://www.forbes.com/sites/billfrist/2021/01/20/nih-director-dr-francis-collins-connecting-the-dots-from-the-human-genome-project-to-the-covid-19-vaccine/?sh=73d4bcc57543

NIH Director Dr. Francis Collins: Connecting The Dots From The Human Genome Project To The COVID-19 Vaccine

Bill Frist

I cover global and domestic health care and health care reform.

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On the most recent episode of A Second Opinion podcast, I asked Dr. Francis Collins if we were going to be prepared for the next pandemic.

“Senator, I sure hope so! This has been the worst pandemic in 102 years, and if we are not able to learn from this and plan for what inevitably will be down the road, then we only have ourselves to blame. We don’t have a great track record there.”

Francis Collins and I have a long professional friendship. We worked closely together from 1998 to 2003 when I was in the United States Senate and he was leading the Human Genome Project, and I have found him to be not only one of the nation’s top scientific minds, but also an exceptional communicator.

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US President George W. Bush (R) presents the 2007 Presidential Medal of Freedom to Human Genome … [+] AFP VIA GETTY IMAGES

Today, as the director of the National Institutes of Health, Collins has a bird’s eye view of the pandemic, our national response, and how the iterative nature of science brought us to be able to respond as well as we have.

The Human Genome Project, an international effort to sequence the human genome, is the only government initiative that I recall coming in early and under budget. While the United States contributed a bit more than half of the budget and the manpower, it was an international effort also involving scientists from the United Kingdom, France, Germany, Japan and China. It was a monstrous effort and Collins served as the project lead, ensuring that all worked together and the genome was completed in 2003—two years ahead of schedule.

“That had never really been tried at that scale before. It was crossing into this territory of Big Science for biology and medicine, but it worked,” Collins told me. The project also launched an era of data release and openness, with all of the human DNA information delivered into the public domain daily. The idea, Collins explained, was that DNA is our shared inheritance and all of us should be able to learn from it.

That mindset—that biomedical research happens faster with collaboration and sharing of data—is responsible for any success we’ve had with the COVID-19 pandemic. While there have been missteps, the technological advances of genomic sequencing and the international data sharing expectations sped our response by months if not years.

“You can draw a direct line from the success of the Genome Project to the fact that we learned so quickly about SARS-CoV-2: what kind of virus this was, what kind of approach might be necessary to go after it,” Collins said. After the Chinese lab released the sequence of the virus in January 2020—a process that takes a good lab just an hour or two now—researchers around the world could begin researching the virus without needing a sample. “That made it possible within 24 hours for the first vaccine design to get started!” Collins said.

The investments the American people made in the Human Genome Project—Collins told me they spent about $3 billion on the project, $400 million of which was on the sequencing itself—have repaid us hundreds of times over in biomedical, technology, computing, and economic advances.

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Yet, one year ago, we still were not prepared for a global pandemic. Even though many of the scientific foundations were there, we have still spent 2020 learning hard lessons in funding, logistics, distribution, and more.

“We have this complacency problem, and we need not slip into that,” Collins told me.

I warned about this complacency in a series of 2005 speeches, noting that, “rapid, voluminous, and essential travel and trade; the decline of staffed hospital beds; and a now heavily urbanized and suburbanized American population dependent as never before upon ‘just in time’ but easily-disrupted networks of services and supply,” had left us unprepared to respond to the unknown, deadly pathogens that would inevitably come.

And come, they have.

Collins had kind words to say about my warnings 15 years ago, but, unfortunately, those speeches didn’t save us from our current reality. “Some listened, maybe some didn’t. Other pressures came along that seemed more urgent for that day’s needs and we kind of forgot about the difference between the important and the urgent,” he observed. “We better not do that this time.”

Instead, he highlighted what we have learned in the past 12 months that should serve us well in the future. We have developed new types of public-private partnerships and set up new funding models to more quickly enable urgent research. But there is more work to do. Collins called for active pathogen surveillance and platforms to quickly spin up development of vaccines, therapeutics, monoclonal antibodies, and diagnostics—at scale.

This work needs to be done around the world, not just at home. Collins and I agree wholeheartedly on this point. Now is our teachable moment: Viruses don’t need visas and pandemics have no borders. The U.S. has a significant leadership role to play here, but we can’t do it alone. “We’re in a circumstance, right now, where the boundaries between countries and cultures are increasingly porous both to ideas and ethical decisions—and viruses!” Collins said.

Accomplishing all of these goals will take purposeful funding, diligence, and consistency. “It’s going to take strong voices like yours and maybe mine to keep putting this in front of leaders of the country and the world,” Collins said. “If you want to save the next group of lives from the next pandemic—maybe it’s influenza, maybe it’s another coronavirus, maybe it’s a filovirus, I don’t know, but it’s coming!—this set of lessons must not be forgotten.”

part3/end

https://www.forbes.com/sites/billfrist/2021/01/20/nih-director-dr-francis-collins-connecting-the-dots-from-the-human-genome-project-to-the-covid-19-vaccine/?sh=73d4bcc57543

https://archive.is/22drG