Greengenes: A Tutorial

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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
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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?
greengenes.lbl.gov
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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 (gt75).

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Who uses Greengenes?

• Clinical researchers
• To study microbes present in a patients 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 Tutorial

• Broadens 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

• 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

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Teacher Resources

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

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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 theyre formed.
• Taxonomies What a taxonomy is and how why
  taxonomists disagree (hence Greengenes using 6
  taxonomies)

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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

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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