Greengenes is a website used by biologists from around the globe to detect and classify microorganisms from their local environments, based upon easily collected DNA samples. For example, Eoin Brodie of Berkeley Lab’s Earth Sciences Division (ESD) is finding natural soil bacteria that prevent toxic heavy metals from entering waterways. He can rapidly analyze DNA samples from subsurface waters by comparing them against the comprehensive Greengenes database hosted in Terry Hazen's Ecology Department at Berkeley Lab.
Greengenes is also aiding Berkeley Lab’s Yvette Piceno in analyzing bacterial content in post-Katrina New Orleans flood waters, and helping other microbiologists at Washington University in searching for intestinal bacteria associated with human obesity. Another application, for DOE’s Mission Focus on Biofuels, will aid in the discovery of microbial communities able to convert cellulose into ethanol.
These projects and others, as well as the recent publications about Greengenes in Applied and Environmental Microbiology and Nucleic Acids Research, have led to increasing web site activity since Greengene's inception in 2003. With a growing number of microbiologists turning to Greengenes to classify their bacterial and archaeal sequences has come a rise in questions from users new to the system. Many users have been confused by the different software options available on the web to determine gene sequences from raw chromatograms, or to align their sequences to each other or to an annotated standard alignment. Others have been uncertain as to which tool to use for taxonomic classification.
ESD’s Todd DeSantis, Greengenes’ database administrator (within Gary Andersen's Molecular Microbial Ecology Group), turned to science educator Jonathan Davies, from James Logan High School in Union City, to develop a straightforward way for new users to find the website on-ramp. Davies is a not only a 2006 Berkeley Lab CSEE Summer Teaching Fellow but is also associated with the Industry Initiatives for Science and Math Education (IISME). (IISME, in its 27th year, places Bay Area teachers into research and industry settings for the summer to make connections between the classroom and the science and technology used by industry.)
In response to DeSantis’s request, Davies has created a tutorial designed to lead a variety of users through the full series of steps necessary to input their bacterial DNA sequences and receive a detailed classification of those sequences back from the Greengenes database.
The tutorial project was conceived in spring of 2006 to expand usage of the Greengenes technology to advanced high school and undergraduate biology students. It has since grown to include a greater audience: anyone looking to classify their bacterial DNA sequences, whether he or she is an experienced, casual, or novice user. It currently includes sample data to allow the novice user a chance to become familiar with the different files used and returned by Greengenes. The sample data can also be used in conjunction with the tutorial to try out the various steps in Greengenes, from aligning sequences up to and through taxonomic classification. Users of the tutorial will find vocabulary and acronyms explained with links to additional information. These include point mutations, chimeras as PCR artifacts, and the six different taxonomies used by Greengenes for classification.
As the tutorial continues to develop, lesson plans will be available to educators to integrate the Greengenes technology directly into their classrooms and laboratories. There will be a slide-show presentation to introduce Greengenes’ taxonomic classification and its tutorial. A series of lessons will be available to lead students through the steps covered in the tutorial and the associated concepts and background information necessary to successfully utilize the technology. Students can also get an introduction to the concepts of alignment and chimeras.
Since Greengenes is periodically expanding its capabilities, the tutorial will grow in steps. For example, it will soon assist users in designing DNA probes for rapid quantification of specific bacterial families. Bioinformatics tools are being developed by ESD summer student Nunut (Alex) Butarbutar to address this challenge. Other associated projects continue to develop, with new data constantly being added to the Greengenes website. For example, Daniel Sam, graduate student collaborator from UC Santa Cruz, is deploying on-line tools by which researchers can compare the bacterial composition of urban aerosols by time and location.
For more information about using Greengenes as an educational tool, e-mail Jonathan Davies.
Note that Davies is one of seven IISME teachers who are being hosted here at Berkeley Lab through CSEE. Each summer, CSEE brings teachers, pre-service teachers, and high school students to Berkeley Lab as part of an outreach to cultivate the next generation of scientists.
