Scientists decode DNA of microbes from humans

As part of the Human Microbiome Project (HMP), scientists at Washington University School of Medicine in St. Louis and their colleagues have decoded the genomes of 178 microbes from the human body.

The researchers discovered novel genes and proteins that contribute to human health and disease, adding a new level of understanding to the complexity and diversity of these organisms. Findings are reported May 21 in the journal Science.

The new research represents a major milestone in the HMP’s study of the “second genome” of humans. The Genome Center at Washington University is a major player in the HMP, having decoded the genomes of more than half of the newly published microbes.

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, many of the microorganisms are necessary for good health but some can cause illness.

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 growing HMP catalog of microbial genomes.

“These genomes are enormously useful because they allow researchers to trace the origin of short stretches of DNA to specific microbes, so now we can begin to see how particular collections of microbes influence health and disease,” says co-author George Weinstock PhD, associate director of Washington University’s Genome Center and a professor of genetics and microbiology. “But we have a long journey ahead of us – there are thousands of organisms in the microbiome and our goal is to produce a complete genome sequence for each one of them.”

Launched in 2008, the HMP is a $157 million, five-year effort, funded by the National Institutes of Health, to unravel 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 from 18 areas of the body, including the digestive tract, mouth, skin, nose and vagina.

“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 Francis S. Collins, MD, PhD, director of the National Institutes of Health. “We are only at the very beginning of a fascinating voyage that will transform how we diagnose, treat and ultimately, prevent many health conditions.”

The HMP 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 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 new proteins in the reference collection – more proteins than there are estimated genes in the human genome.

In addition to Washington University’s Genome Center, genome sequencing work for the project was conducted at the Human Genome Sequencing Center, Baylor College of Medicine, Houston; The J. Craig Venter Institute, Rockville, Md.; and the Broad Sequencing Platform, Broad Institute of MIT/ Harvard, Cambridge, Mass.

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 HMP data may also be accessed from its Data Analysis and Coordination Center website,

Washington University School of Medicine’s 2,100 employed and volunteer faculty physicians also are the medical staff of Barnes-Jewish and St. Louis Children’s hospitals. The School of Medicine is one of the leading medical research, teaching and patient care institutions in the nation, currently ranked fourth in the nation by U.S. News & World Report. Through its affiliations with Barnes-Jewish and St. Louis Children’s hospitals, the School of Medicine is linked to BJC HealthCare.