Navigation Links
New models predict where E. coli strains will thrive
Date:11/18/2013

Bioengineers at the University of California, San Diego have used the genomic sequences of 55 E. coli strains to reconstruct the metabolic repertoire for each strain. Surprisingly, these reconstructions do an excellent job of predicting the kind of environment where each strain will thrive, the researchers found.

Their analysis, published in the Nov. 18, 2013 early edition of the Proceedings of the National Academy of Sciences, could prove useful in developing ways to control deadly E. coli infections and to learn more about how certain strains of the bacteria become virulent.

And when "nasty new versions" of E. coli appear, the metabolic models may someday help researchers quickly identify and characterize these new strains, said Bernhard Palsson, professor of bioengineering at UC San Diego Jacobs School of Engineering and a corresponding author on the paper.

The reconstructions map out all the genes, reactions and products of metabolism for each strain and allow the researchers to probe their coordinated functionality. Each strain's metabolic capabilities, the researchers discovered, correspond to specific environmental niches. Commensal or "friendly" E. coli strains also can be distinguished from pathogenic strains using this technique.

"This paper shows that you can predict the microenvironmental niche where human pathogenic strains of E. coli grow, whether it's in your bladder or your stomach, or your blood or elsewhere, based on these sequences," Palsson said.

Jonathan Monk, a nanoengineering graduate student in the Jacobs School of Engineering and lead author of the paper, said that the metabolic reconstructions might also help researchers figure out ways to deprive pathogenic E. coli of the nutrients they need, "so that you can prevent them from getting an advantage in that niche, and maybe better control an infection that way."

The first E. coli strain was sequenced 15 years ago, but the plummeting cost of gene sequencing has made a plethora of other E. coli genomes available to compare with this first "model" strain. The wealth of genome data, Palsson said, has led some researchers to wonder whether the model organism fully represents the E. coli species.

In the PNAS study, Palsson and colleagues identified a core metabolic network shared by all the strains, as well as all the differences in metabolic content among the strains. Most of these differences appear to be in the ability to break down various nutrients, said Adam Feist, a project scientist in the UC San Diego Jacobs School of Engineering, alumnus of the Palsson lab in the bioengineering department, and the other corresponding author on the paper.

In retrospect, this variety isn't too surprising, he said, given the number of "diverse environmentson the skin, inside the body, outside in the dirt that E. coli are found in."

In future studies, Feist said, the researchers hope to "drill deeper" into this variation and explore whether strains that contain the same metabolic content "use that similar content differently."

The researchers found that their models could also identify E. coli strains that lack the genes to help them manufacture certain essential compounds, such as niacin. This phenomenon, called auxotrophy, often goes hand in hand with virulence. Many experiments have shown that when these missing genes are restored, the bacteria become less virulent. "So finding out why these strains have become auxotrophs could shed a lot of light on how an organism becomes a pathogen," Monk said.

The predictive success of the metabolic models has the team thinking about applying the method to other bacteria such as Staphylococcus aureus, said Palsson. "We intend to move aggressively forward with categorizing many human pathogens in this way."


'/>"/>

Contact: Daniel Kane
dbkkane@eng.ucsd.edu
858-534-3262
University of California - San Diego
Source:Eurekalert

Related biology technology :

1. HemoShear to Develop Human Cancer Models to Improve Industry Success Rates in New Anticancer Drug Development
2. New Advances and Opportunities in Managing Pain: Translational Animal Models, New Webinar Hosted by Xtalks
3. Cellular Dynamics International Expands MyCell Products Line with Disease Models, Genetic Engineering Patents
4. Advancing Preclinical Predictions, Making Faster Clinical Decisions with Cancer Models and Preclinical Imaging - World Pharma Congress this June in Philadelphia
5. University of Colorado Cancer Center Study Shows that Bitter Melon Juice Prevents Pancreatic Cancer in Mouse Models
6. GNS Healthcare Joins Orion Bionetworks to Develop Predictive Models for Multiple Sclerosis and Other Diseases
7. Organovo Partners With ZenBio to Create 3D Tissue Models
8. Karyopharm Therapeutics Announces Oral Presentation at the American College of Rheumatology (ACR) on the use of Selective Inhibitors of Nuclear Export (SINE) CRM1 Antagonists in preclinical models of Systemic Lupus Erythematosus (SLE)
9. Harvards Wyss Institute models a human disease in an organ-on-a-chip
10. Isis And Collaborators Alleviate Disease In Animal Models Of Myotonic Dystrophy
11. A new imaging system produces 3-D models of monuments using unmanned aircraft
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/22/2016)... ... June 22, 2016 , ... Quantitative ... business incubator and current participant in the Phase 1 Ventures program, is leveraging ... , Quantitative Radiology Solutions helps physicians make better treatment decisions by quantifying ...
(Date:6/22/2016)... (PRWEB) , ... June 21, 2016 , ... New light-based ... cutting into the tissue — promise to enable both compact, wearable devices for point-of-care ... even deeper under the skin. , Recent work and visionary future directions are detailed ...
(Date:6/22/2016)... SAN DIEGO , June 22, 2016 /PRNewswire/ ... that has developed a testing platform designed specifically ... the formation of their scientific advisory board (SAB). ... of directors, the SAB is chartered to advise ... infectious disease assay platform. Led by Dr. ...
(Date:6/22/2016)... June 22, 2016 On Tuesday, June ... 4,843.76, up 0.14%; the Dow Jones Industrial Average advanced 0.14% ... 2,088.90, up 0.27%. The gains were broad based as five ... has initiated coverage on the following equities: Minerva Neurosciences Inc. ... PTLA ), Trevena Inc. (NASDAQ: TRVN ), ...
Breaking Biology Technology:
(Date:4/28/2016)... First quarter 2016:   , ... the first quarter of 2015 The gross margin was ... 18.8) and the operating margin was 40% (-13) Earnings ... flow from operations was SEK 249.9 M (21.2) , ... SEK 7,000-8,500 M. The operating margin for 2016 is ...
(Date:4/19/2016)... 2016 The new GEZE SecuLogic ... web-based "all-in-one" system solution for all door components. It ... the door interface with integration authorization management system, and ... The minimal dimensions of the access control and the ... installations offer considerable freedom of design with regard to ...
(Date:4/14/2016)... BioCatch ™, the global ... the appointment of Eyal Goldwerger as CEO. ... Goldwerger,s leadership appointment comes at a time of significant ... of its platform at several of the world,s largest ... unique cognitive and physiological factors, is a winner of ...
Breaking Biology News(10 mins):