Navigation Links
New method for identifying microbes

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.


'"/>

Source:DOE/Brookhaven National Laboratory


Related biology news :

1. Color-blind method opens new doors in DNA sequencing
2. New imaging method gives early indication if brain cancer therapy is effective, U-M study shows
3. Studies reveal methods viruses use to sidestep immune system
4. An entropy-based gene selection method for cancer classification using microarray data
5. New methods of gene delivery using lasers
6. Breakthrough method in nanoparticle synthesis paves the way for new pharmaceutical and biomedical applications
7. Shift of weather patterns necessitates rethinking of reforestation methods
8. Scientists use manufacturing methods to reconstruct mastodon
9. Researchers develop promising new gene network analysis method
10. New method shows it is possible to grow bone for grafts within a patients body
11. Researchers develop new method for facile identification of proteins in bacterial cells
Post Your Comments:
*Name:
*Comment:
*Email:


(Date:6/15/2016)... , June 15, 2016 ... market report titled "Gesture Recognition Market by Application Market - Global ... 2016 - 2024". According to the report, the  global ... billion in 2015 and is estimated to grow ... 48.56 billion by 2024.  Increasing application ...
(Date:6/7/2016)... , June 7, 2016  Syngrafii Inc. and ... business relationship that includes integrating Syngrafii,s patented LongPen™ ... project. This collaboration will result in greater convenience ... credit union, while maintaining existing document workflow and ... ...
(Date:6/2/2016)... , June 2, 2016   The Weather Company ... announcing Watson Ads, an industry-first capability in which consumers will ... being able to ask questions via voice or text and ... Marketers have long sought an ... consumer, that can be personal, relevant and valuable; and can ...
Breaking Biology News(10 mins):
(Date:6/23/2016)... ... June 23, 2016 , ... UAS LifeSciences, one of the ... brand, UP4™ Probiotics, into Target stores nationwide. The company, which has been manufacturing ... to its list of well-respected retailers. This list includes such fine stores as ...
(Date:6/23/2016)... ... June 23, 2016 , ... Charm Sciences, Inc. is ... has received AOAC Research Institute approval 061601. , “This is another AOAC-RI approval ... Bob Salter, Vice President of Regulatory and Industrial Affairs. “The Peel Plate methods ...
(Date:6/23/2016)... ... , ... STACS DNA Inc., the sample tracking software company, today announced that ... joined STACS DNA as a Field Application Specialist. , “I am thrilled that ... of STACS DNA. “In further expanding our capacity as a scientific integrator, Hays brings ...
(Date:6/23/2016)... 2016 On Wednesday, June 22, 2016, ... 0.22%; the Dow Jones Industrial Average edged 0.27% lower to ... down 0.17%. Stock-Callers.com has initiated coverage on the following equities: ... (NASDAQ: NKTR ), Aralez Pharmaceuticals Inc. (NASDAQ: ... BIND ). Learn more about these stocks by accessing their ...
Breaking Biology Technology: