Navigation Links
Bioinformatics technology developed at Argonne provides new insight into microbial activities

ARGONNE, Ill. (March 14, 2008) -- 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 Energys (DOE) Argonne National Laboratory. This technology has already been used to identify subtle differences in the metabolic processes of microbial communities.

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 projects 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.


Contact: Steve McGregor
DOE/Argonne National Laboratory

Related biology news :

1. Yale scientists use nanotechnology to fight E. coli
2. Voice Biometrics Gains Traction as Most Accurate and Convenient Technology to Secure Customer Privacy
3. M2SYS Partners with SecuGen Corporation to Support Market Leading Hamster Plus Fingerprint Reader with Auto-On Technology
4. Silicon Valley Technology Leaders LaserCard Corporation and Tesla Motors Sign LaserPass Secure Access Deal
5. Nanotechnology: Whats that?
6. UCs NIH grant brings technology from outer space to playgrounds
7. BIO-key(R) International to Showcase Deployed Biometric Security Applications at 2007 Biometric Technology Expo
8. Cogent Systems and Northrop Grumman Reach Agreement to Settle Automated Fingerprint Identification Technology Suit and Create Strategic Alliance
9. UCLA/VA partners with ASU to advance biosensor technology for urinary tract infections
10. Herr receives Heinz Award for Technology, the Economy and Employment
11. Singapore National Science and Technology Awards
Post Your Comments:
(Date:11/12/2015)... 12, 2015  Arxspan has entered into an ... Harvard for use of its ArxLab cloud-based suite ... The partnership will support the institute,s efforts to ... research information internally and with external collaborators. The ... managing the Institute,s electronic laboratory notebook, compound and ...
(Date:11/10/2015)... About signature verification Signature ... identify and verify the identity of an individual ... secure and accurate method of authentication and is ... because each individual,s signature is highly unique. Signature ... signature of an individual is compared and matched ...
(Date:11/2/2015)... MENLO PARK, Calif. , Nov. 2, 2015 /PRNewswire/ ... to $9 million to provide preclinical development services to ... Under the contract, SRI will provide scientific expertise, modern ... a wide variety of preclinical pharmacology and toxicology studies ... --> --> The PREVENT Cancer Drug ...
Breaking Biology News(10 mins):
(Date:11/27/2015)... , Nov. 27, 2015 /PRNewswire/--  Mallinckrodt plc (NYSE: ... today that it has closed the sale of its ... Guerbet (GBT- NYSE Euronext) in a transaction valued at ... manufacturing facilities and a total of approximately 1,000 employees ... St. Louis area. This entire ...
(Date:11/26/2015)... , November 26, 2015 ... --> Accutest Research Laboratories, a ... Research Organization (CRO), has formed a ... Center - Temple Health for joint ... ,     (Photo: ) , ...
(Date:11/25/2015)... , Nov. 25, 2015  PharmAthene, Inc. (NYSE MKT: ... adopted a stockholder rights plan (Rights Plan) in an ... loss carryforwards (NOLs) under Section 382 of the Internal ... --> PharmAthene,s use of its NOLs could be ... as defined in Section 382 of the Code. In ...
(Date:11/25/2015)... and HOLLISTON, Mass. , Nov. ... (Nasdaq: HART ), a biotechnology company developing bioengineered ... Jim McGorry will present at the LD ... 2015 at 2:30 p.m. PT. The presentation will be ... 30 days. Management will also be available at the ...
Breaking Biology Technology: