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New technique shows what microbes eat


The gutless marine worm Olavius algarvensis was used as a test case for the new technique. This worm does not have a digestive system and instead is fed by a community of symbiotic bacteria living in the worm. Photo courtesy of Christian Lott/NC State University

By Brooke Baitinger, UPI

Some microbes feed from the bacteria they carry around in their bodies, which can make it tough to figure out what exactly fuels them.

Researchers from North Carolina State University and the University of Calgary have developed a new technique to determines exactly what certain microbes have eaten. That information can give a more in-depth look at the metabolism and physiology within microbial communities and the role these microscopic life forms play in environments such as the open ocean or the human intestinal tract.

Understanding microbial communities is vital to comprehending animal and plant health and disease, according to Manuel Kleiner, an assistant professor in the Department of Plant and Microbial Biology at NC State. He said it's also key to understanding important environmental processes such as decomposition of organic matter and nutrient cycling in soils and oceans.

Specifically, the new technique -- outlined in a paper published this week in the journal PNAS -- identifies what substrate a microbe has consumed.

Researchers used a mass spectrometer to measure the mass of molecules derived from the microbes in a community. Then they linked the microbes with their substrates using the newly developed software program.

Connecting microbes and substrates is the basis for carbon stable isotope ratios, or the ratios between naturally occurring forms of carbon with different masses. Each material has a specific ratio of these two isotopes, which identifies the material like a fingerprint or a signature.

Nature contains carbon-12, which is the most abundant form, and carbon-13, which has one more neutron than carbon-12.

The new algorithm links carbon isotope ratios of substrates in microbes to ratios found in the microbes themselves.

"Our method is based on the concept that you are what you eat," Kleiner said in a press release. "If there is a food source with a specific isotope signature and we find a microbe with that same specific isotopic signature, we can make the connection between the two."

A similar technique is used by archeological anthropologists, who can determine the type of diet a person ate by analyzing isotope ratios from hair or bone fragments, he said.

The researchers actually used their own hair as a calibration standard to correct for errors that can occur when measuring the mass of the molecules, he said.

The researchers tested the algorithm by examining 20 pure culture samples, showing that the software gave measurements consistent with mass spectrometry standards. They also tested for individual signatures for different species within the same complex community in a sample with different microorganisms.

The researchers then tested the metabolism of the symbiotic relationship between a gutless marine worm and the multiple bacteria it hosts.

The data from the study is publicly available, and the software -- implemented in Java -- has been made freely available for other researchers to download and use.


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Technology - U.S. Daily News: New technique shows what microbes eat
New technique shows what microbes eat
Technology - U.S. Daily News
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