A new study of the human microbiome 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.
“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
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.
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.
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
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
Harvard Chan authors included Gholamali Rahnavard
and Eric Franzosa.
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,
Harvard T.H. Chan School of Public Health
Institute of MIT and Harvard
University of Maryland School of Medicine
National Institutes of Health Human Microbiome