Innovation and Partnerships Office

PhyloChip: DNA Microarray for Rapid Profiling of Microbial Populations IB-2229

If interested in this technology, please contact Second Genome, Inc. our exclusive commercial licensee.

Berkeley Lab’s DNA Microarray for Rapid Profiling of Microbial Populations, also called PhyloChip.


  • Monitoring airborne bacteria for bioterrorism surveillance
  • Tracking microbial changes in the atmosphere due to climate change
  • Detecting harmful and beneficial organisms in water or soil samples
  • Monitoring bacterial populations during environmental bioremediation
  • Identifying bacteria and archaea in medical samples without culturing
  • Enabling source tracking of pathogens by public health agencies


  • Quickly and accurately identifies microbes in complex samples
  • Analyzes microbial DNA samples from any environmental source
  • Simultaneously detects most known microorganisms (>8000 strains tested in parallel)
  • Offers the option to analyze the rRNA to determine the most metabolically active organisms in a sample
  • Detects low-abundance organisms that would be missed by conventional culturing or sequencing
  • Identifies microorganisms most responsive to changes in environmental parameters
  • Reduces the chances of misidentifying a specific microorganism


Gary Andersen, Todd DeSantis, and their colleagues at Berkeley Lab have invented a fast DNA microarray (PhyloChip) that is unique in its ability to identify multiple bacterial and archaeal organisms from complex microbial samples. Formerly, researchers relied on bacterial cultures to identify the microbes present in an environmental or medical sample. Culture media would be exposed to a sample, and anything that grew in the culture would be counted. The problem with this older method is that most organisms—up to 99% of the bacteria in a sample—can’t survive in a culture. The DNA microarray developed at Berkeley Lab is a much more rapid, comprehensive, and accurate means for sample testing without any culturing required.

The Berkeley Lab PhyloChip probes samples for the 16S rRNA gene, which is involved in making proteins and is found in all bacteria and archaea. Capable of analyzing samples from any source—such as air, water, soil, blood, or tissue—this microarray quickly and accurately identifies known and unknown organisms. Unknown organisms are classified based on their similarities to known microbes.

Multiple probes on the array provide increased accuracy and greater confidence in detection, also identifying low-abundance microbes that would be missed by conventional sequencing methods. The high-density microarray format—with a combination of multiple probes and a paired mismatch-control probe for each perfect-match probe—significantly reduces the chances of misidentifying a specific microorganism.

In a recent test, the quality of the results from this microarray were demonstrated by cataloging the bacteria in air samples taken from two Texas cities. Over 1,800 types of bacteria were found in these samples. Before this study, no one had a sense of the diversity of microbes in the air. PhyloChip has also already been used to study biological degradation of toxic chemicals, bioremediation of uranium, microbial composition of the atmosphere due to climate change, and the pathogenic colonization of lungs in intubated patients. NASA has also used the phylochip to study air quality in Jet airliners.

STATUS: Published Patent Application WO/2008/130394 available at and US-2009-0291858-A1 available at USPTO.

Available for collaborative research in the field of identifying and / or classifying fungi only. For all other uses, contact Second Genome, Inc. the exclusive commercial licensee of this technology.


Brodie, E. L., DeSantis, T.Z., Joyner D.C., Baek, S.M., Larsen, J.T., Andersen, G.L., Hazen, T.C., Richardson, P.M., Herman, D.J., Tokunaga, T.K., Wan, J.M, Firestone, M.K. Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation. Applied Environmental Microbiology. Vol. 72: 6288-98. 2006.

Brodie, E. L., DeSantis, T.Z, Parker, J.P., Zubietta, I.X., Piceno, Y.M., Andersen., G.L. Urban Aerosols Harbor Diverse and Dynamic Bacterial Populations. Proceedings of the National Academy of Sciences of the United States of America. Vol. 104: 299-304. 2007.

DeSantis, T. Z., Brodie, E.L., Moberg, J.P., Zubieta, I.X., Piceno, Y.M., Andersen, G.L., High-density Universal 16S rRNA Microarray Analysis Reveals Broader Diversity Than Typical Clone Library When Sampling the Environment. Microbiology Ecology. Vol. 53: 371-83. 2007.

Flanagan, J. L., Brodie, E.L, Weng, L., Lynch, S.V., Garcia, O., Brown, R., Hugenholtz, P., DeSantis, T.Z., Andersen, G.L., Wiener-Kronish, J.P, Bristow, J. Loss of Bacterial Diversity During Antibiotic Treatment of Intubated Patients Colonized with Pseudomonas Aeruginosa. Journal of Clinical Microbiology. Vol. 45: 1954-1962. 2007.

Moissl, C., Osman, S., La Duc, M.T., Dekas, A., Brodie, E., Desantis, T., Venkateswaran, K. Molecular bacterial community analysis of clean rooms where spacecraft are assembled. FEMS Microbiology Ecology. Vol. 62: 131. 2007.