Innovation and Partnerships Office

Berkeley Lab’s PhyloChip Enables Tracking of Bacterial Dangers

In 1675 Antonie van Leeuwenhoek asked, “what’s out there?,” before he discovered the existence of microorganisms. Now, over 300 years later, researchers at Lawrence Berkeley National Laboratory (LBNL) are able to accurately and quickly test for over 8,000 bacterial species with a device that fits into a person’s hand – a microbial detection power previously unknown.

This new technology, called PhyloChip, enables scientists to study bacterial communities, their interactions, and how they change over time. This capability is important because deep, sudden changes in the structure of a bacterial community could represent dangers in the form of an airborne biological terrorist attack, an epidemic caused by contaminated water or soil, or hazardous atmospheric alterations caused by climate change.

Invented by Gary Andersen, Todd DeSantis, and colleagues at LBNL, PhyloChip is a DNA microarray unique in its ability to identify multiple bacterial species and organisms from complex microbial samples. Because PhyloChip produces results within hours, numerous samplings of a specific environment can be conducted on a daily basis, enabling scientists to track the progress of a certain microorganism over a short period of time.

PhyloChip was the environment category winner of The Wall Street Journal’s 2008 Technology Innovation Awards and Affymetrix, Inc. is currently distributing the technology to 28 beta-test sites under a limited license agreement.

Recently, LBNL’s PhyloChip was tested by cataloging the bacteria in air samples taken from San Antonio and Austin, Texas. Over 1,800 types of bacteria were found! Before this study, no one comprehended the diversity of airborne microbes. By identifying microbial communities typically inhaled by inhabitants of large U.S. cities, PhyloChip can help monitor air quality. The bacterial census from this study will help the Department of Homeland Security differentiate between normal and suspicious fluctuations in airborne microbes.

Formerly, microbiologists have relied on bacterial cultures to identify the microbes present in an environmental or medical sample, but most organisms—up to 99% of the bacteria in a sample—don’t survive in a culture. PhyloChip is a much more rapid, comprehensive, and accurate means for sample testing without culturing. As reported in the Journal of Clinical Microbiology (2007), PhyloChip was key to discovering that a loss of bacterial diversity due to antibiotic treatments was directly associated with the development of pneumonia in ventilated patients exposed to a certain common strain of bacteria.

The LBNL technology has also proven valuable in helping preserve a healthy environment. As published in Applied And Environmental Microbiology (2006) PhyloChip could prevent a less-soluble form of uranium from converting to a soluble form, thus forestalling the migration of this radioactive material and optimizing site remediation efforts.  Monitoring contaminated sites where the existing bacteria were naturally immobilizing uranium, the PhyloChip was able to identify several synergistically acting microbes.  By creating conditions more favorable for these bacteria it may be possible to increase the efficiency of immobilization.

The Berkeley Lab Phylochip makes possible discoveries that may change all disciplines touched by microbiology, including medicine, immunology, and environmental biology and takes Leeuwenhoek’s initial discovery to a whole new level.

Developed by: Gary Andersen, Todd DeSantis,Eoin Brodie, and Yvette Piceno