The Phylochip Wins Again!

In a stiff worldwide competition held by the Wall Street Journal, ESD staff scientist Gary Andersen and a team of ESD researchers (Todd DeSantis, Eoin Brodie, and Yvette Piceno) won the overall bronze medal—and first prize in the Environment category—for their work in developing the Berkeley Lab PhyloChip. These WSJ awards for Technology Innovation were announced in late September 2008, following just a few months after the PhyloChip won an R&D 100 award (in July 2008), and signify that, for 2008, in the judgment of the Wall Street Journal, the PhyloChip was the top environmental technology in the world.

The ESD team beat out major companies like Xerox, OnStar, and Tata Motors—CEOs from companies as far away as India came to the October 2008 awards ceremony in Redwood City, California, to accept runner-up awards. With this award, Berkeley Lab became the only national laboratory ever to make it into the top three (as well as being the overall winner of the Environment category). The judges included Robert Drost, the Director of Sun Microsystems Lab, and Anthony Komaroff, Professor at Harvard Medical Scholl and Editor in Chief of Harvard Health Publications.

The PhyloChip is a microchip that, by analyzing DNA, is able to identify thousands of different varieties of bacteria that might be present in air, water, soil, blood, or tissue samples. The PhyloChip can detect potentially disease-causing bacteria without the lengthy process of growing cultures. And unlike other genetic-testing methods, it can distinguish thousands of different pathogens simultaneously. With the PhyloChip, scientists can recognize, in a matter of hours, up to 8,700 different organisms in a single sample.

At the Redwood City award ceremony, Andersen described the thinking behind the PhyloChip’s development:

The idea of our PhyloChip came from a very basic premise: We are intimately surrounded by a community of microbes that affects our lives in both positive and negative ways. Life as we know it would not be the same without our microbial friends providing most of the oxygen that we breathe, cleaning up our spills, and giving us great-tasting food and drink. But the only time we really pay attention to microbes is when their interactions are out of balance, causing disease or fouling our machinery.

Within the short time that we have used this device in real-world environments, we have identified mechanisms for infection in ventilator-associated pneumonia, leading to changes in standards of patient care. We were also able to show how combinations of several bacteria species were effective in cleaning up toxic spills in Tennessee.

Furthermore, by identifying what microbes are present and which ones are the most active, we are currently using the PhyloChip to look at water quality in California state beaches and determine when the risk to exposure to pathogens is the highest. We are looking at what microbes most effectively break down plant-cell material to create a more efficient next generation of biofuels. And we are looking at how changes in bacterial composition within our bodies affect our health.

In all this work, we have been fortunate to have the support of Berkeley Lab, and the Earth Sciences Division within the Lab, to enable our ideas to become a reality.

During the selection process for these awards, the ESD team continued to find new applications for the PhyloChip. ESD post-doc Kristin DeAngelis selected the PhyloChip to pinpoint 147 soil bacteria responding to root growth from native California grasses. It turns out that this is a relatively small subset (only 7%) of the entire bacterial community. DeAngelis also compared the PhyloChip-generated data against an older, more laborious technique, T-RFLP, and found that while the two agreed well on the subset percentage, only the PhyloChip enabled identification of the taxa in flux. Her article will be presented in the Nature publication, International Society of Microbial Ecology Journal (ISME).

ISME will also publish the results of an international effort to discover the bacteria and archaea inhabiting the extreme environments in Antarctica. The research team opted for the PhyloChip after the costly method of DNA sequencing proved too insensitive for detecting the entire spectrum of microbial populations in these unique environments. In other work, Tetsu Tokunaga and others in ESD, collaborating with UC Berkeley’s Mary Firestone, Don Herman, and Rebecca Daly, have used the PhyloChip in monitoring the bioremediation of uranium-contaminated sediment. This research was published recently in Environmental Science and Technology.

Additional PhyloChip projects are under way. An investigation of the cause of diseases in coral reefs is being conducted by Shini Sunagawa, in an ESD collaboration with UC Merced. ESD’s Eric Dubinsky and Shariff Osman are surveying the pathogenic bacteria at public beaches, and ESD’s Cindy Wu is finding sources of sewage contamination in urban creeks. And finally, ESD’s Kelly Wrighton and John Coates have used the PhyloChip to find microbial communities capable of producing electricity within fuel cells. Their findings were recently published online by ISME Journal.

Peer-reviewed articles describing or utilizing the PhyloChip

• Brodie, E.L., T.Z. DeSantis, et al. (2007). "Urban aerosols harbor diverse and dynamic bacterial populations." Proc. Natl. Acad. Sci. U.S.A, 104(1): 299-304.
• Brodie, E.L., T.Z. DeSantis, et al. (2006). "Application of a High-Density Oligonucleotide Microarray Approach To Study Bacterial Population Dynamics during Uranium Reduction and Reoxidation." Appl. Environ. Microbiol., 72(9): 6288-98.
• Chivian, D., E.L. Brodie, et al. (2008). "Environmental genomics reveals a single-species ecosystem deep within Earth." Science, 322(5899): 275-8.
• DeAngelis, K.M., E.L. Brodie, et al. (2008). "Selective progressive response of soil microbial community to wild oat roots." ISME J. (in revision).
• DeSantis, T.Z., I. Dubosarskiy, et al. (2003). "Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA." Bioinformatics, 19(12): 1461-8.
• DeSantis, T.Z., C.E. Stone, et al. (2005). "Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray." FEMS Microbiol. Lett., 245(2): 271-8.
• DeSantis, T.Z., E.L. Brodie, et al. (2007). "High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment." Microb. Ecol., 53(3): 371-83.
• Flanagan, J.L., E.L. Brodie, et al. (2007). "Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa." J. Clin. Microbiol., 45(6): 1954-62.
• Kuramae, E. E., H. Gamper, et al. (2008). "Prokaryotic succession in chalk grasslands after field abandonment."  In preparation.
  Lin, L. H., P. L. Wang, et al. (2006). "Long-term sustainability of a high-energy, low-diversity crustal biome." Science, 314(5798): 479-82.
• Sunagawa, S., T.Z. DeSantis, Y.M. Piceno, E.L. Brodie, M.K. DeSalvo, C.R. Voolstra, E. Weil, G.L. Andersen, and M. Medina (2008). "Bacterial diversity and white plague disease-associated community changes in the Caribbean Coral Montastraea faveolata."  ISME Journal (in press).
• Tokunaga, T. K., J. Wan, et al. (2008). "Influences of Organic Carbon Supply Rate on Uranium Bioreduction in Initially Oxidizing, Contaminated Sediment." Environ Sci Technol. (in press).
• Wilson, K. H., W. J. Wilson, et al. (2002). "High-density microarray of small-subunit ribosomal DNA probes." Appl Environ Microbiol 68(5): 2535-41.
• Wrighton, K. C., P. Agbo, et al. (2008). "A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells." ISME Journal, 2(11): 1146-56.
• Yergeau, E., S. Kang, et al. (2008). "Functional microarray analysis of nitrogen and carbon cycling genes across an Antarctic latitudinal transect." ISME Journal (in press).