Featured Research

from universities, journals, and other organizations

Bioinformatics Technology Provides New Insight Into Microbial Activities

Date:
March 18, 2008
Source:
DOE/Argonne National Laboratory
Summary:
Scientists may gain a new insight into the relationship between viruses and their environments thanks to a new computational technology. This technology has already been used to identify subtle differences in the metabolic processes of microbial communities.

Scientists may gain a new insight into the relationship between viruses and their environments thanks to a new computational technology developed by researchers at the U.S. Department of Energy's (DOE) Argonne National Laboratory. This technology has already been used to identify subtle differences in the metabolic processes of microbial communities.

Related Articles


The ability to determine such differences may help scientists detect environmental changes at early stages and identify previously unknown pathways for treating disease.

The researchers analyzed the frequency distribution of more than 14 million microbial and viral sequences from almost 90 different ecological communities, called metagenomes. By doing so, they hoped to produce a biological profile for the samples taken from diverse environments ranging from underground mines to sea and fresh water.

"Metagenomics enables the DNA from all microbes to be sequenced at once, without any culturing," said Robert Edwards, a computational biologist at Argonne and San Diego State University and one of the project's principal investigators. "Such an approach was impossible even a decade ago."

While the researchers had expected to find similar lifestyles among the viral metagenomes in every environment, they instead found that the metagenomes have distinctive metabolic profiles. Researchers may be able to use these profiles in the future to answer questions about the viral dynamics in, for example, the lungs of cystic fibrosis patients.

"Argonne has become a world leader in metagenomics," said Edwards. "The bioinformatics technology developed by Argonne researchers and their collaborators is being used by hundreds of researchers worldwide. This work demonstrates the practical basis for the multimillion-dollar effort by the National Institutes of Health to understand the benign and malign roles of microbes in health and disease."

As the use of metagenomics has become increasingly common, scientists have had to address the challenge of analyzing an enormous number of genomic sequences. To ease this process, scientists at Argonne and the Fellowship for Interpretation of Genomes (FIG) developed a system that contains all known DNA and protein sequences. Using this directory, known as SEED, biologists can identify matches between metagenomes and profiles already in the SEED database.

For this study, DNA sequences first were analyzed by using a high-throughput pipeline called the metagenomics RAST (Rapid Annotation using Subsystem Technology) server developed by researchers from Argonne in collaboration with FIG, the University of Chicago, San Diego State University and Hope College.

"Comparing such a huge number of metagenomes is an enormous computational task," said Rick Stevens, a principal investigator in the project and associate laboratory director of Computing, Environment, and Life Science at Argonne. "This automated technology revolutionizes the steps needed to acquire an accurately annotated genome."

The sequences then were compared to the SEED platform by using the compute cluster at the National Microbial Pathogen Data Resource. The database allows an overview of the microbial communities and the ability to focus on one metabolic area and detect differences in the proteins being used by the microbes in each environment.

"The initial analysis took months of computer time," said Stevens. "We eventually determined that more than 1 million sequences from the microbial metagenomes and more than 500,000 from the viral metagenomes were significantly similar to functional genes within the SEED."

The research was funded by the Gordon and Betty Moore Foundation Marine Microbial Initiative, the National Science Foundation, a Department of Commerce ATP grant, a National Research Initiative Competitive Grant from the USDA Cooperative State Research, Education and Extension Service, the National Institute of Allergy and Infectious Diseases, the National Institutes of Health and the Department of Health and Human Services.

The results have been accepted for publication in the journal Nature (doi.org/10.1038/nature06810).


Story Source:

The above story is based on materials provided by DOE/Argonne National Laboratory. Note: Materials may be edited for content and length.


Cite This Page:

DOE/Argonne National Laboratory. "Bioinformatics Technology Provides New Insight Into Microbial Activities." ScienceDaily. ScienceDaily, 18 March 2008. <www.sciencedaily.com/releases/2008/03/080314112235.htm>.
DOE/Argonne National Laboratory. (2008, March 18). Bioinformatics Technology Provides New Insight Into Microbial Activities. ScienceDaily. Retrieved November 27, 2014 from www.sciencedaily.com/releases/2008/03/080314112235.htm
DOE/Argonne National Laboratory. "Bioinformatics Technology Provides New Insight Into Microbial Activities." ScienceDaily. www.sciencedaily.com/releases/2008/03/080314112235.htm (accessed November 27, 2014).

Share This


More From ScienceDaily



More Plants & Animals News

Thursday, November 27, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

New Dinosaur Species Found in Museum Collection

New Dinosaur Species Found in Museum Collection

Reuters - Innovations Video Online (Nov. 27, 2014) A British palaeontologist has discovered a new species of dinosaur while studying fossils in a Canadian museum. Pentaceratops aquilonius was related to Triceratops and lived at the end of the Cretaceous Period, around 75 million years ago. Jim Drury has more. Video provided by Reuters
Powered by NewsLook.com
Classic Hollywood Memorabilia Goes Under the Hammer

Classic Hollywood Memorabilia Goes Under the Hammer

Reuters - Entertainment Video Online (Nov. 26, 2014) The iconic piano from "Casablanca" and the Cowardly Lion suit from "The Wizard of Oz" fetch millions at auction. Sara Hemrajani reports. Video provided by Reuters
Powered by NewsLook.com
Pet Dogs to Be Used in Anti-Ageing Trial

Pet Dogs to Be Used in Anti-Ageing Trial

Reuters - Innovations Video Online (Nov. 26, 2014) Researchers in the United States are preparing to discover whether a drug commonly used in human organ transplants can extend the lifespan and health quality of pet dogs. Video provided by Reuters
Powered by NewsLook.com
From Popcorn To Vending Snacks: FDA Ups Calorie Count Rules

From Popcorn To Vending Snacks: FDA Ups Calorie Count Rules

Newsy (Nov. 25, 2014) The US FDA is announcing new calorie rules on Tuesday that will require everywhere from theaters to vending machines to include calorie counts. Video provided by Newsy
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:

Strange & Offbeat Stories


Plants & Animals

Earth & Climate

Fossils & Ruins

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins