Greengenes: A Tutorial Taxonomic Classification of Bacteria Using DNA Sequences Created by: Jonathan Davies James Logan High School Union City, CA

Background: 1735 - Linneaus, Systema Naturae Scientific Name: Genus species Yesterday: Classification based on morphology, physiology & embryology Today: Classification based on DNA Prokaryotes can be identified/classified based on a single gene!!

What is Greengenes? greengenes.lbl.gov

What is Greengenes? An up-to-date database of known 16S rRNA gene sequences A web based tool used to classify cloned bacterial DNA sequences Allows users to create their own local database Allows users to compare sequences to each other and to landmarks in the Greengenes database

The 16S rRNA gene A gene found only in prokaryotes It can be species specific - differentiating one bacterial strain from another It codes for the small subunit of the ribosome

High Throughput Analysis A single gram of soil can contain 103-106 distinct taxa!! Greengenes is designed to quickly and efficiently analyze large numbers of sequences (>75).

Who uses Greengenes? Clinical researchers: To study microbes present in a patient’s throat, lungs, GI tract, etc. Environmental microbiologists: To compare the microbial communities from different locales To see how a microbial community changes over time To monitor the effectiveness of bioremediation efforts.

Greengenes Tutorial Broadens target audience to include: Advanced high school students AP classes Biotech classes Science Fair projects Undergraduate researchers

Greengenes Tutorial

Greengenes Tutorial A step by step parallel to Greengenes designed to walk the user through: Alignment of sequences to database sequences Removal of chimeric sequences Classification of sequences Includes Sample Data to allow the user to test out each step on a low throughput basis Lesson to Walk through Greengenes Using the Sample Data

Teacher Resources Lesson using sample data to gain practice with Greengenes PowerPoint introduction for teacher and students Sample Data to practice using Greengenes

Teacher Resources Embedded within the Tutorial are pages to cover special topics: Point Mutations Near Neighbors & Type Strains (for making distance trees) Chimeras: What they are and how they’re formed. Taxonomies: What a taxonomy is and how & why taxonomists disagree (hence Greengenes using 6 taxonomies)

Future of Tutorial Hands-on lessons to explain algorithms Alignment Chimeras Taxonomies Sample data sets to use in ecology unit Water quality Food poisoning Bioremediation

Acknowledgements Todd DeSantis: Greengenes Database Administrator Gary Andersen, PhD: PI, Molecular Microbial Ecology Group Eoin Brodie, PhD: Microbial Ecologist Yvette Piceno, PhD: Microbial Ecologist Alex Butar: Bioinformatics CSEE: Rollie Otto, Michael Thibodeau, Tom Knight IISME: Patti Forster, Kaye Storm Bechtel Foundation