Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


New Method for Identifying Microbes


Genomic “tags” quickly catalog species, distinguish pathogens from harmless relatives

Scientists at the U.S. Department of Energy’s Brookhaven National Laboratory have developed a new, high-throughput technique for identifying the many species of microorganisms living in an unknown “microbial community.” The method, described in the March 2006 issue of Applied Environmental Microbiology, has many applications — from assessing the microbes present in environmental samples and identifying species useful for cleaning up contamination to identifying pathogens and distinguishing harmless bacteria from potential bioterror weapons.

“Microbial communities are enormously diverse and complex, with hundreds of species per milliliter of water or thousands per gram of soil,” said Brookhaven biologist Daniel (Niels) van der Lelie, lead author of the study. “Elucidating this complexity is essential if we want to fully understand the roles microbes play in global cycles, make use of their enormous metabolic capabilities, or easily identify potential threats to human health.”

Growing cultures of microbes to identify species is slow and error prone as the culture conditions often screen out important members of the community. Sequencing entire genomes, while highly specific and informative, would be too labor intensive and costly. So scientists have been searching for ways to identify key segments of genetic code that are short enough to be sequenced rapidly and can readily distinguish among species.

The Brookhaven team has developed just such a technique, which they call “single point genome signature tagging.” Using enzymes that recognize specific sequences in the genetic code, they chop the microbial genomes into small segments that contain identifier genes common to all microbial species, plus enough unique genetic information to tell the microbes apart.

In one example, the scientists cut and splice pieces of DNA to produce “tags” that contain 16 “letters” of genetic code somewhat “upstream” from the beginning of the gene that codes for a piece of the ribosome — the highly conserved “single point” reference gene. By sequencing these tags and comparing the sequenced code with databases of known bacterial genomes, the Brookhaven team determined that this specific 16-letter region contains enough unique genetic information to successfully identify all community members down to the genus level, and most to the species level as well.

“Sequencing is expensive, so the shorter the section you can sequence and still get useful information, the better,” van der Lelie said. “In fact, because these tags are so short, we ‘glue’ 10 to 30 of them together to sequence all at one time, making this a highly efficient, cost-effective technique.”

For tag sequences that can’t be matched to an already sequenced bacterial genome (of which there are only a couple hundred), the scientists can use the tag as a primer to sequence the entire attached ribosomal gene. This gene is about 1400 genetic-code-letters long, so this is a more time-consuming and expensive task. But since ribosomal genes have been sequenced and cataloged from more than 100,000 bacterial species, this “ribotyping” technique makes use of a vast database for comparison.

“If there’s still no match,” said van der Lelie, “then the tag probably identifies a brand new species, which is also very interesting!”

In another test with possible applications for identifying agents used in bioterror attacks, the technique also clearly discriminated between closely related strains of Bacillus cereus, a pathogenic soil microbe, and Bacillus anthracis, the bacterial cause of anthrax.

This technique could also help assess how microbial community composition responds to changes in the environment. Such information might help identify which combinations of species would be best suited to, say, sequestering carbon or cleaning up radiological contamination.

This study represents just one application of genome signature tagging, a technique developed at and patented by Brookhaven Lab. Brookhaven scientists have also used genome “tags” to identify the sites where regulatory proteins bind to DNA (more) . This research could greatly speed the process of unraveling the role these proteins play in turning on and off certain genes in different types of cells — as well as what might go awry in conditions like cancer.

This research was funded by the Office of Biological and Environmental Research within the U.S. Department of Energy’s Office of Science and by Brookhaven’s Laboratory Directed Research and Development funds.

Karen McNulty Walsh | EurekAlert!
Further information:

More articles from Life Sciences:

nachricht Novel mechanisms of action discovered for the skin cancer medication Imiquimod
21.10.2016 | Technische Universität München

nachricht Second research flight into zero gravity
21.10.2016 | Universität Zürich

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: New 3-D wiring technique brings scalable quantum computers closer to reality

Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.

"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...

Im Focus: Scientists develop a semiconductor nanocomposite material that moves in response to light

In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.

A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...

Im Focus: Diamonds aren't forever: Sandia, Harvard team create first quantum computer bridge

By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.

"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...

Im Focus: New Products - Highlights of COMPAMED 2016

COMPAMED has become the leading international marketplace for suppliers of medical manufacturing. The trade fair, which takes place every November and is co-located to MEDICA in Dusseldorf, has been steadily growing over the past years and shows that medical technology remains a rapidly growing market.

In 2016, the joint pavilion by the IVAM Microtechnology Network, the Product Market “High-tech for Medical Devices”, will be located in Hall 8a again and will...

Im Focus: Ultra-thin ferroelectric material for next-generation electronics

'Ferroelectric' materials can switch between different states of electrical polarization in response to an external electric field. This flexibility means they show promise for many applications, for example in electronic devices and computer memory. Current ferroelectric materials are highly valued for their thermal and chemical stability and rapid electro-mechanical responses, but creating a material that is scalable down to the tiny sizes needed for technologies like silicon-based semiconductors (Si-based CMOS) has proven challenging.

Now, Hiroshi Funakubo and co-workers at the Tokyo Institute of Technology, in collaboration with researchers across Japan, have conducted experiments to...

All Focus news of the innovation-report >>>



Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

Agricultural Trade Developments and Potentials in Central Asia and the South Caucasus

14.10.2016 | Event News

World Health Summit – Day Three: A Call to Action

12.10.2016 | Event News

Latest News

Resolving the mystery of preeclampsia

21.10.2016 | Health and Medicine

Stanford researchers create new special-purpose computer that may someday save us billions

21.10.2016 | Information Technology

From ancient fossils to future cars

21.10.2016 | Materials Sciences

More VideoLinks >>>