Featured Research

from universities, journals, and other organizations

New models predict where E. coli strains will thrive

Date:
November 18, 2013
Source:
University of California - San Diego
Summary:
Bioengineers 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.

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.

Related Articles


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 chemical engineering graduate student in the Jacobs School of Engineering Department of NanoEngineering 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 environments -- on 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."


Story Source:

The above story is based on materials provided by University of California - San Diego. The original article was written by Daniel Kane. Note: Materials may be edited for content and length.


Cite This Page:

University of California - San Diego. "New models predict where E. coli strains will thrive." ScienceDaily. ScienceDaily, 18 November 2013. <www.sciencedaily.com/releases/2013/11/131118155953.htm>.
University of California - San Diego. (2013, November 18). New models predict where E. coli strains will thrive. ScienceDaily. Retrieved December 20, 2014 from www.sciencedaily.com/releases/2013/11/131118155953.htm
University of California - San Diego. "New models predict where E. coli strains will thrive." ScienceDaily. www.sciencedaily.com/releases/2013/11/131118155953.htm (accessed December 20, 2014).

Share This


More From ScienceDaily



More Plants & Animals News

Saturday, December 20, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Researchers Test Colombian Village With High Alzheimer's Rates

Researchers Test Colombian Village With High Alzheimer's Rates

AFP (Dec. 19, 2014) In Yarumal, a village in N. Colombia, Alzheimer's has ravaged a disproportionately large number of families. A genetic "curse" that may pave the way for research on how to treat the disease that claims a new victim every four seconds. Duration: 02:42 Video provided by AFP
Powered by NewsLook.com
Monarch Butterflies Descend Upon Mexican Forest During Annual Migration

Monarch Butterflies Descend Upon Mexican Forest During Annual Migration

Reuters - Light News Video Online (Dec. 19, 2014) Millions of monarch butterflies begin to descend onto Mexico as part of their annual migration south. Rough Cut (no reporter narration) Video provided by Reuters
Powered by NewsLook.com
The Best Protein-Filled Foods to Energize You for the New Year

The Best Protein-Filled Foods to Energize You for the New Year

Buzz60 (Dec. 19, 2014) The new year is coming and nothing will energize you more for 2015 than protein-filled foods. Fitness and nutrition expert John Basedow (@JohnBasedow) gives his favorite high protein foods that will help you build muscle, lose fat and have endless energy. Video provided by Buzz60
Powered by NewsLook.com
Birds Might Be Better Meteorologists Than Us

Birds Might Be Better Meteorologists Than Us

Newsy (Dec. 19, 2014) A new study suggests a certain type of bird was able to sense a tornado outbreak that moved through the U.S. a day before it hit. 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