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MEDICAL: GENETICS :
PUBLICATIONS:
NIH Human Microbiome Project Researchers Publish
First Genomic Collection of Human Microbes
Date: Thu, 20 May 2010 14:19:06 -0400
From: "NIH OLIB (NIH/OD)" <[log in to unmask]>
To: [log in to unmask]
Subject: NIH Human Microbiome Project Researchers Publish
First Genomic Collection of Human Microbes
U.S. Department of Health and Human Services
NATIONAL INSTITUTES OF HEALTH NIH News
National Human Genome Research Institute (NHGRI)
<http://www.nhgri.nih.gov/>
Embargoed for Release: Thursday, May 20, 2010, 2 p.m. EDT
CONTACT:
Geoff Spencer, NHGRI
301-402-0911
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NIH HUMAN MICROBIOME PROJECT RESEARCHERS PUBLISH
FIRST GENOMIC COLLECTION OF HUMAN MICROBES
Diversity of Human Microbes Greater Than Previously Predicted
The Human Microbiome Project (HMP) today published an analysis of 178
genomes from microbes that live in or on the human body. The researchers
discovered novel genes and proteins that serve functions in human health
and disease, adding a new level of understanding to what is known about
the complexity and diversity of these organisms.
The human microbiome consists of all the microorganisms that reside in or
on the human body. Outnumbering cells in the human body by 10 to 1, some
of the microorganisms cause illnesses, but many are necessary for good
health. Currently, researchers can grow only some of the bacteria, fungi
and viruses in a laboratory setting. However, new genomic techniques can
identify minute amounts of microbial DNA in an individual and determine
its identity by comparing the genetic signature to known sequences in the
project's data base. The paper is published in the May 21 issue of the
journal Science.
"This initial work lays the foundation for this ambitious project and is
critical for understanding the role that the microbiome plays in human
health and disease," said National Institutes of Health Director Francis
S. Collins, M.D., Ph.D. "We are only at the very beginning of a
fascinating voyage that will transform how we diagnose, treat and
ultimately, prevent many health conditions."
Launched in 2008 as part of the NIH Common Fund's Roadmap for Medical
Research, the HMP is a $157 million, five-year effort that will implement
a series of increasingly complicated studies that reveal the interactive
role of the microbiome in human health.
The 178 microbial genomes in this report launch the HMP reference
collection that eventually will total approximately 900 microbial genomes
of bacteria, viruses and fungi. These data will then be used by HMP
researchers to characterize the microbial communities found in samples
taken from healthy human volunteers and, later, those with specific
illnesses. Samples are currently being collected for HMP from five areas
of the body: the digestive tract, the mouth, the skin, the nose and the
vagina.
"Although this is only the first step in making HMP medically useful, we
already have learned surprising things about the diversity and complexity
of the microorganisms that live in and on our body," said Jane Peterson,
Ph.D., associate director of the NHGRI Division of Extramural Researcher
and a leader of the HMP effort. "The next stages of this coordinated study
will begin to associate the presence or absence of specific
micro-organisms with various states of health and illness."
Researchers also conducted a preliminary survey to gain insights into the
function of some of the newly identified genes and proteins unique to
individual microbial strains. For instance, researchers found previously
unknown proteins produced by bacteria that live in the stomach that may
cause gastric ulceration, a hole in the stomach lining. In addition, they
found a small number of newly identified novel proteins associated with
how sugars and amino acids are metabolized.
Researchers also evaluated the microbial diversity present in the HMP
reference collection. For example, they found 29,693 previously
undiscovered, unique proteins in the reference collection - more proteins
than there are estimated genes in the human genome. They compared their
results to the same number of previously sequenced microbial genomes
randomly selected from public databases. In the microbial genome from
public databases, they found 14,064 novel proteins. These data, the
researchers say, suggest that the HMP reference collection has nearly
twice the amount of microbial diversity than is represented by microbial
genomes already in public databases.
One of the primary goals of the HMP reference collection is to expand
researchers' ability to interpret data from metagenomic studies.
Metagenomics is the study of a collection of genetic material (genomes)
from a mixed community of organisms. Comparing metagenomic sequence data
with genomes in the reference collection can help researchers determine
whether they are novel or already existing sequences.
To evaluate whether the reference collection of genomes was meeting the
goal above, the researchers compared 16.8 million microbial sequences
found in public databases to the genome sequences in the HMP reference
collection. They found that 62 genomes in the reference collection showed
similarity with 11.3 million microbial sequences in public databases and
6.9 million of these -- about 41 percent -- correspond with genome
sequences in the reference collection.
This analysis demonstrates that genomes sequenced as part of the reference
collection add directly to an understanding of the human microbiome.
However, researchers cautioned that at least one-third of the metagenomic
sequences are still not represented by any genome in the reference
collection and that this analysis focused only on the gastrointestinal
tract. The authors added that additional genomes likely exist in other
body sites and the completion of the reference collection should address
many of the remaining organisms not accounted for in this analysis.
The initial stage of the HMP, which includes the current study, focused on
bacteria, but future genome sequencing and human microbiome studies also
will capture information about more complex microbes and viruses. The
effort so far also has allowed researchers to create a framework for data
resources and standards. In addition, the project is supporting the
development of innovative technologies and computational tools,
coordination of data analysis, and an examination of some of the ethical,
legal and social implications of human microbiome research.
Genome sequencing work for the project is done by the HMP-funded
large-scale sequencing centers: the Human Genome Sequencing Center, Baylor
College of Medicine, Houston; Washington University Genome Sequencing
Center, Washington University School of Medicine, St. Louis; The J. Craig
Venter Institute, Rockville, Md.; and the Broad Sequencing Platform, Broad
Institute of MIT/ Harvard, Cambridge, Mass.
The HMP is currently funding pilot demonstration projects by researchers
that will sample the microbiomes of healthy volunteers and volunteers with
specific diseases over the next year. This will allow researchers to study
changes in the microbiome at particular body sites in healthy controls
compared to patients affected by diseases. These studies will use samples
collected from seven areas of the body: the digestive tract, the mouth,
the skin, the nose, the vagina, the blood and the male urethra.
Genomes sequenced as part of the HMP and those generated by unrelated
projects are publicly available from the
National Library of Medicine's
National Center for Biotechnology Information
part of NIH, at
<http://www.ncbi.nlm.nih.gov/genomes/MICROBES/microbial_taxtree.html>
HMP data may also be accessed from its
Data Analysis and Coordination Center website,
<http://hmpdacc.org/>
More information about the Human Microbiome Project is available at
<http://www.nihroadmap.nih.gov/hmp/>
An illustration showing the body sites that will be sampled as part of the
Human Microbiome Project is available at:
<http://www.genome.gov/pressDisplay.cfm?photoID=20163>
A high resolution image of the bacteria, Entercoccus faecalis, a microbe
that lives in the human gut, is available in color at
<http://www.genome.gov/pressDisplay.cfm?photoID=20023>
or in black and white at
<http://www.genome.gov/pressDisplay.cfm?photoID=20024>
The Human Microbiome Project is funded through the Common Fund, and
managed by the NIH Office of the Director in partnership with the National
Institute of Allergy and Infectious Diseases, National Institute of
Arthritis and Musculoskeletal and Skin Diseases, National Cancer
Institute, National Institute of Dental and Craniofacial Research,
National Institute of Diabetes and Digestive and Kidney Diseases and
National Human Genome Research Institute, all part of NIH. The NIH Common
Fund encourages collaboration and supports a series of exceptionally high
impact, trans-NIH programs. Common Fund programs are designed to pursue
major opportunities and gaps in biomedical research that no single NIH
Institute could tackle alone, but that the agency as a whole can address
to make the biggest impact possible on the progress of medical research.
Additional information about the NIH Common Fund can be found at
<http://commonfund.nih.gov>
The National Institutes of Health (NIH) -- The Nation's Medical Research
Agency -- includes 27 Institutes and Centers and is a component of the
U.S. Department of Health and Human Services. It is the primary federal
agency for conducting and supporting basic, clinical and translational
medical research, and it investigates the causes, treatments, and cures
for both common and rare diseases. For more information about NIH and its
programs, visit
<http://www.nih.gov>
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<http://www.nih.gov/news/health/may2010/nhgri-20.htm>
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