greengenes: a tutorial taxonomic classification of bacteria using dna sequences created by: jonathan...
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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!!
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What is Greengenes?
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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
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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
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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).
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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.
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Greengenes TutorialBroadens target audience to include:
– Advanced high school students• AP classes• Biotech classes• Science Fair projects
– Undergraduate researchers
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Greengenes Tutorial
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Greengenes Tutorial
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• A step by step parallel to Greengenes designed to walk the user through:
a) Alignment of sequences to database sequences
b) Removal of chimeric sequencesc) 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
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• Lesson using sample data to gain practice with Greengenes
• PowerPoint introduction for teacher and students
• Sample Data to practice using Greengenes
Teacher Resources
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• 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
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• 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
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