Public Release: 

Thousands of new microbial communities identified in human body

Study sheds light on differences unique to individuals' microbes

Harvard T.H. Chan School of Public Health

Key Takeaways:

  • Scientists used a wealth of new data from DNA sequencing tools to study the human microbiome in unprecedented depth and detail

  • The new information provides insights as to how microbes work in concert with each other, within specific individuals, across various sites in the body, and over time

Boston, MA - A new study of the human microbiome -- the trillions of microbial organisms that live on and within our bodies -- has analyzed thousands of new measurements of microbial communities from the gut, skin, mouth, and vaginal microbiome, yielding new insights into the role these microbes play in human health.

The study, from researchers at Harvard T.H. Chan School of Public Health, Broad Institute of MIT and Harvard, and University of Maryland School of Medicine, presents a three-fold expansion of data from the National Institutes of Health Human Microbiome Project, providing unprecedented depth and detail about human microbial diversity. The new information allows researchers to identify differences that are unique to an individual's microbes -- just like some human genome variants are unique to each individual -- and track them across the body and over time.

The study will be published online September 20, 2017 in Nature.

"This study has given us the most detailed information to date about exactly which microbes and molecular processes help to maintain health in the human microbiome," said Curtis Huttenhower, associate professor of computational biology and bioinformatics at Harvard Chan School, associate member of the Broad Institute, and senior author of the study.

This study is an expanded second phase of the Human Microbiome Project, originally launched in 2007 to identify and characterize human microbes, explore microbes' relationship to health and disease, and develop computational tools to analyze the microbes. The microbiome has been linked to everything from allergies to cancer.

The researchers analyzed 1,631 new samples from 265 individuals, from diverse body sites and at multiple points in time. The scientists used DNA sequencing tools that allowed them to precisely identify which organisms are present in various body sites, as well as what they might be able to do. Examining microbes at multiple time points further allowed them to determine which parts of the community might change slowly, rapidly, or stay relatively stable over time.

The findings:

  • Provide one of the largest profiles of non-bacterial members--viruses and fungi--of the microbiome across the body

  • Identified microbes with specific strains within each body site

  • Profile the biochemical activity that allows microbes to help maintain human health

  • Identify how the microbes and their biochemistry change over time

Huttenhower said the new study also emphasizes how much scientists still don't know about the makeup and function of the human microbiome. Learning more about it will take time, he said.

"Just as sequencing one human genome, without information about variability or context, didn't immediately lead to extensive new drugs or therapies, so too will we need to look at the microbiome with an extremely fine lens, in many different contexts, so that we can understand and act on its specific, personalized changes in any individual disease or condition," said Jason Lloyd-Price, postdoctoral associate at the Broad Institute, postdoctoral fellow at Harvard Chan School, and lead author of the study.

He added that the study also provides a large data resource to the scientific community that will help drive future research, discoveries, and the development of new methods in studying the human microbiome.

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Other Harvard Chan authors included Gholamali Rahnavard and Eric Franzosa.

Support for the study came from National Institutes of Health grants U54DK10255, U01HG006537, U01HG004866, U54HG004969, U54HG004973, U54AI084844, U54HG004968, U54HG003079, and the Crohn's & Colitis Foundation of America.

"Strains, functions, and dynamics in the expanded Human Microbiome Project," Jason Lloyd-Price, Anup Mahurkar, Gholamali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, Arthur Brady, Heather H. Creasy, Carrie McCracken, Michelle G. Giglio, Daniel McDonald, Eric A. Franzosa, Rob Knight, Owen White, Curtis Huttenhower, Nature, online September 20, 2017, doi: 10.1038/nature23889

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About Harvard T.H. Chan School of Public Health

Harvard T.H. Chan School of Public Health brings together dedicated experts from many disciplines to educate new generations of global health leaders and produce powerful ideas that improve the lives and health of people everywhere. As a community of leading scientists, educators, and students, we work together to take innovative ideas from the laboratory to people's lives--not only making scientific breakthroughs, but also working to change individual behaviors, public policies, and health care practices. Each year, more than 400 faculty members at Harvard Chan School teach 1,000-plus full-time students from around the world and train thousands more through online and executive education courses. Founded in 1913 as the Harvard-MIT School of Health Officers, the School is recognized as America's oldest professional training program in public health.

About the Broad Institute of MIT and Harvard

Broad Institute of MIT and Harvard was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods, and data openly to the entire scientific community.

Founded by MIT, Harvard, Harvard-affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff, and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to http://www.broadinstitute.org.

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