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

2. 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!!

3. What is Greengenes?
greengenes.lbl.gov

4. 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

5. 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

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

7. 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.

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

9. Greengenes Tutorial

10. 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

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

12. 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)

13. 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

14. 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