Corporate Banner
Satellite Banner
Genomics
Scientific Community
 
Become a Member | Sign in
Home>News>This Article
  News
Return

Venter Institute Scientists Sequence 178 Microbial Reference Genomes Associated with the Human Body

Published: Friday, May 28, 2010
Last Updated: Friday, May 28, 2010
Bookmark and Share
Consortium members of the NIH's Human Microbiome project finds greater microbial diversity in human microbiome than previously known.

Researchers from the J. Craig Venter Institute, a not-for-profit genomic research organization, have published (along with other members of the National Institutes of Health (NIH) Human Microbiome Jumpstart Reference Strains Consortium), a catalog of 178 microbial reference genomes isolated from the human body.

Other members of the Consortium are: Baylor College of Medicine Human Genome Sequencing Center, the Broad Institute, and the Genome Center at Washington University. The paper is being published in the May 21 issue of the journal Science.

The human body is teeming with a variety of microbial species. This collective community is called the human microbiome. The role these microbes play in human health and disease is still relatively unknown but likely very important.

The NIH Human Microbiome Project was launched in 2007, as part of the National Institutes of Health’s (NIH) Common Fund’s Roadmap for Medical Research. It 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 HMP Jumpstart Consortium has been charged with selecting the microbial strains to sequence from the following body sites: gastrointestinal tract, oral cavity, urogenital/vaginal tract, skin and respiratory tract; with creating standards for sequencing and annotation; and ensuring the rapid release of information to the scientific community.

The Consortium’s goal is to ultimately produce 900 reference genomes. So far the group has produced and released into the public domain 239 genomes. The 178 genomes represented in this publication are completely annotated and analyzed. The sequencing was conducted using mostly the Roche-454 sequencing platform along with some traditional Sanger sequencing. The team compared the sequenced reference genomes to human metagenomic data in the public domain to find new genes and proteins, to ascertain some function for these genes and to assign metagenomic data to species.

From the analysis of 547,968 predicted proteins, the team found 29,987 unique proteins. This data set was compared to a randomly selected data set of 178 previously sequenced prokaryotic genomes found in the public database GenBank and there were fewer unique genes in this data set than in the human microbiome. This is said to be a unique finding and suggests that there is greater microbial diversity in the human microbiome than was previously known.

The group found some novel gene functions unique to particular microbial strains in the reference genome set. While the group cautioned that this was preliminary data and more work was needed on gene functions, some initial insights into important functions were gleaned.

One of the main goals of having HMP reference genomes is to help interpret and understand metagenomic data. Since the HMP reference genomes were isolated from humans and were not in metagenomic data sets, the group was uncertain if these reference genomes would aid in identifying metagenomic sequences. However, in comparing 16.8 million sequences, the team found that 62 of the HMP reference genomes recruited 11.3 million sequences, and of these, 6.9 million sequences recruited most closely to the HMP reference genomes. Thus, having the HMP reference genomes allowed for 20 to 40% of metagenomic sequences to be identified.

This analysis shows that the HMP reference genomes are aiding substantially in the understanding of the human microbiome. However, the group added that there is still much work to be done in fully understanding the microbiome, and achieving the goal of 900 sequenced reference genomes is necessary for a more complete understanding.

The group concluded that while this initial catalog focused on bacteria, future efforts will concentrate on adding eukaryotic microbes and viruses since these are both found in the human microbiome. As well, the group will continue their work in developing standards for sequencing unculturable strains, strain selection criteria, and providing online access to these large datasets, among many issues.

The corresponding author, JCVI’s Karen E. Nelson, Ph.D., said, “This is a major study that moves us in the right direction to understanding the complex microbiota associated with the human body, and outlines how we benefit from this relationship.  We will continue to learn more about the impact of these species in health and disease conditions.” Nelson also added that the consortium anticipates several additional significant publications on the human microbiome in the near future.


Further Information
Access to this exclusive content is for Technology Networks Premium members only.

Join Technology Networks Premium for free access to:

  • Exclusive articles
  • Presentations from international conferences
  • Over 2,500+ scientific posters on ePosters
  • More than 3,700+ scientific videos on LabTube
  • 35 community eNewsletters


Sign In



Forgotten your details? Click Here
If you are not a member you can join here

*Please note: By logging into TechnologyNetworks.com you agree to accept the use of cookies. To find out more about the cookies we use and how to delete them, see our privacy policy.

Related Content

JCVI Awarded 5 Year, Approximately $25 Million NIH Grant to Establish GCID
Center will utilize next generation genomic sequencing and analysis technologies to better understand infectious disease pathogens, and create resource for the research community.
Saturday, June 07, 2014
137 Marine Microbial Genomes from Cultured Samples are Sequenced
Research gives clearer picture of inhabitants living in ocean surface and gleans insights into how they adapt and survive.
Thursday, November 18, 2010
Castor Bean Genome Published by Research Team Including Scientists from the Venter Institute
A research team published the sequence and analysis of the castor bean genome in Nature Biotechnology.
Wednesday, August 25, 2010
JCVI Researchers Clone and Engineer Bacterial Genomes in Yeast and Transplant Genomes Back into Bacterial Cells
New methods allow for engineering of bacterial chromosomes and the creation of modified bacterial species; should also play key role in boot up of synthetic cell.
Friday, August 21, 2009
J. Craig Venter Institute Researchers Publish Significant Advance in Genome Assembly Technology
Researchers publish paper describing a significant advance in genome assembly in which the team can now assemble the whole bacterial genome in one step.
Monday, December 08, 2008
First Individual Diploid Human Genome Published by Researchers at J. Craig Venter Institute
Sequence reveals that human to human variation is substantially greater than earlier estimates.
Thursday, September 06, 2007
JCVI Scientists Publish First Bacterial Genome Transplantation Changing One Species to Another
Research is important step in further advancing field of synthetic genomics
Thursday, June 28, 2007
J. Craig Venter Institute Announces Management Team and Organizational Structure
The Institute will no longer be organized under the two research divisions TIGR and TCAG, but will now encompass an administrative team and several research groups.
Friday, April 13, 2007
CEO of a Newly Expanded J. Craig Venter Institute to Speak at SEQNSYNTECH
Craig Venter became president and CEO of a newly expanded J. Craig Venter Institute after it absorbed the Institute for Genomic Research and the J. Craig Venter Science Foundation.
Monday, October 16, 2006
Scientific News
Poor Survival Rates in Leukemia Linked to Persistent Genetic Mutations
For patients with an often-deadly form of leukemia, new research suggests that lingering cancer-related mutations – detected after initial treatment with chemotherapy – are associated with an increased risk of relapse and poor survival.
Searching Big Data Faster
Theoretical analysis could expand applications of accelerated searching in biology, other fields.
Growing Hepatitis C in the Lab
Recent discovery allows study of naturally occurring forms of hepatitis C virus (HCV) in the lab.
Inciting an Immune Attack on Cancer Cells
A new minimally invasive vaccine that combines cancer cells and immune-enhancing factors could be used clinically to launch a destructive attack on tumors.
Reprogramming Cancer Cells
Researchers on Mayo Clinic’s Florida campus have discovered a way to potentially reprogram cancer cells back to normalcy.
Genetic Overlapping in Multiple Autoimmune Diseases May Suggest Common Therapies
CHOP genomics expert leads analysis of genetic architecture, with eye on repurposing existing drugs.
Surprising Mechanism Behind Antibiotic-Resistant Bacteria Uncovered
Now, scientists at TSRI have discovered that the important human pathogen Staphylococcus aureus, develops resistance to this drug by “switching on” a previously uncharacterized set of genes.
How DNA ‘Proofreader’ Proteins Pick and Edit Their Reading Material
Researchers from North Carolina State University and the University of North Carolina at Chapel Hill have discovered how two important proofreader proteins know where to look for errors during DNA replication and how they work together to signal the body’s repair mechanism.
Fat in the Family?
Study could lead to therapeutics that boost metabolism.
Tissue Bank Pays Dividends for Brain Cancer Research
Checking what’s in the bank – the Brisbane Breast Bank, that is – has paid dividends for UQ cancer researchers.
Skyscraper Banner

Skyscraper Banner
Go to LabTube
Go to eposters
 
Access to the latest scientific news
Exclusive articles
Upload and share your posters on ePosters
Latest presentations and webinars
View a library of 1,800+ scientific and medical posters
2,500+ scientific and medical posters
A library of 2,500+ scientific videos on LabTube
3,700+ scientific videos
Close
Premium CrownJOIN TECHNOLOGY NETWORKS PREMIUM FREE!