The Evolution of Microbes and Their Genomes: A Phylogenomic Perspective

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The Evolution of Microbes and Their Genomes A
Phylogenomic Perspective

• Jonathan A. Eisen
• October 3, 2009

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Nothing in biology makes sense except in the
light of evolution. T. Dobzhansky (1973)
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Eisen Lab - Phylogenomics of Novelty
Origin of New Functions and Processes
Genome Dynamics

• Evolvability
• Repair and recombination processes
• Intragenomic variation

• New genes
• Changes in old genes
• Changes in pathways

Species Evolution

• Phylogenetic history
• Vertical vs. horizontal descent
• Needed to track gain/loss of processes, infer
  convergence

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Phylogenomic Analysis

• Evolutionary reconstructions greatly improve
  genome analyses
• Genome analysis greatly improves evolutionary
  reconstructions
• There is a feedback loop such that these should
  be integrated

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56.1 The Global Ecosystems Compartments are
Connected by the Flow of Elements
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26.23 Some Would Call It Hell These Archaea
Call It Home
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Human commensals
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Deep Sea Ecosystems
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Fleischmann et al. 1995
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Whole Genome Shotgun Sequencing
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Assemble Fragments
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From http//genomesonline.org
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Major Microbial Sequencing Efforts

• Coordinated, top-down efforts
• Fungal Genome Initiative (Broad/Whitehead)
• Gordon and Betty Moore Foundation Marine
  Microbial Genome Sequencing Project
• Sanger Center Pathogen Sequencing Unit
• NHGRI Human Gut Microbiome Project
• NIH Human Microbiome Program
• White paper or grant systems
• NIAID Microbial Sequencing Centers
• DOE/JGI Community Sequencing Program
• DOE/JGI BER Sequencing Program
• NSF/USDA Microbial Genome Sequencing
• Covers lots of ground and biological diversity

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Genome Sequences Have Revolutionized Microbiology

• Predictions of metabolic processes
• Better vaccine and drug design
• New insights into mechanisms of evolution
• Genomes serve as template for functional studies
• New enzymes and materials for engineering and
  synthetic biology

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rRNA Tree of Life
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The Tree is not Happy
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As of 2002

• At least 40 phyla of bacteria

Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Based on Hugenholtz, 2002
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As of 2002

• At least 40 phyla of bacteria
• Genome sequences are mostly from three phyla

Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Based on Hugenholtz, 2002
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As of 2002

• At least 40 phyla of bacteria
• Genome sequences are mostly from three phyla
• Some other phyla are only sparsely sampled

Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Based on Hugenholtz, 2002
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As of 2002

• At least 40 phyla of bacteria
• Genome sequences are mostly from three phyla
• Some other phyla are only sparsely sampled
• Same trend in Archaea

Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Based on Hugenholtz, 2002
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Need for Tree Guidance Well Established

• Common approach within some eukaryotic groups
• Many small projects funded to fill in some
  bacterial or archaeal gaps
• Phylogenetic gaps in bacterial and archaeal
  projects commonly lamented in literature

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• NSF-funded Tree of Life Project
• A genome from each of eight phyla

• At least 40 phyla of bacteria
• Genome sequences are mostly from three phyla
• Some other phyla are only sparsely sampled
• Solution I sequence more phyla

Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Eisen, Ward, Badger, Wu, Wu, et al.
Chloroflexi
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The Tree of Life is Still Angry
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Major Lineages of Actinobacteria
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• At least 100 phyla of bacteria
• Genome sequences are mostly from three phyla
• Most phyla with cultured species are sparsely
  sampled
• Lineages with no cultured taxa even more poorly
  sampled
• Solution - use tree to really fill gaps

Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Well sampled phyla
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http//www.jgi.doe.gov/programs/GEBA/pilot.html
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GEBA Pilot Project Overview

• Identify major branches in rRNA tree for which no
  genomes are available
• Identify a cultured representative for each group
• Grow gt 200 of these and prep. DNA
• Sequence and finish 100
• Annotate, analyze, release data
• Assess benefits of tree guided sequencing

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Some Lessons From GEBA
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GEBA Lesson 1

• rRNA Tree of Life is a Useful Guide and Genomes
  Improve Resolution

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rRNA Tree of Life
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GEBA Lesson 2

• Phylogenetically Guided Selection Can Help
  Annotate Other Genomes

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Predicting Function

• Identification of motifs
• Small sequence elements that code for some
  general activity (e.g., ATPase)
• Homology/similarity based methods
• Identify longer stretches of similarity to genes
  with known function
• Evolutionary reconstructions

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Evolutionary Functional Prediction
Based on Eisen, 1998 Genome Res 8 163-167.
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Recent Functional Changes

• Phylogenomic functional prediction may not work
  well for very newly evolved functions
• Screen genomes for genes that have changed
  recently
• Examples
• Acquisition (e.g., LGT)
• Unusual dS/dN ratios
• Rapid evolutionary rates
• Duplication and divergence

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Non homology functional prediction

• Many genes have homologs in other species but no
  homologs have ever been studied experimentally
• Non-homology methods can make functional
  predictions for these
• Example correlated presence/absence of genes
  across species

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Most/All Functional Prediction Improves w/ Better
Phylogenetic Sampling

• Better definition of protein family sequence
  patterns
• Greatly improves comparative and evolutionary
  based predictions
• Conversion of hypothetical into conserved
  hypotheticals
• Linking distantly related members of protein
  families
• Improved non-homology prediction

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GEBA Lesson 3

• Phylogenetically Guided Selection Can Help Study
  Uncultured Organisms

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Great Plate Count Anomaly
Microscope
Culturing
Count
Count
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Great Plate Count Anomaly
Microscope
Culturing
Count
Count
ltltltlt
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Great Plate Count Anomaly
DNA
Microscope
Culturing
Count
Count
ltltltlt
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PCR Saves the Day
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Sequencing and uncultured microbes I rRNA
surveys
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rRNA A Phylogenetic Anchor to Determine Whos
Out There
Biology not similar enough
Eisen et al. 1992
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Perna et al. 2003
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Environmental Shotgun Sequencing
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Novel Form of Phototrophy
Beja et al. 2000
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Binning challenge
A B C D E F G
T U V W X Y Z
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Glassy Winged Sharpshooter

• Feeds on xylem sap
• Vector for Pierces Disease
• Potential bioterror agent

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Xylem and Phloem
From Lodish et al. 2000
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Wu et al. 2006 PLoS Biology 4 e188.
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Sharpshooter Shotgun Sequencing
shotgun
Collaboration with Nancy Morans lab
Wu et al. 2006 PLoS Biology 4 e188.
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Sulcia makes vitamins and cofactors
Baumannia makes amino acids
Wu et al. 2006 PLoS Biology 4 e188.
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Binning challenge
A B C D E F G
T U V W X Y Z
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GEBA Lesson 4

• We have still only scratched the surface of
  microbial diversity

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Protein Family Rarefaction Curves

• Take data set of multiple complete genomes
• Identify all protein families using MCL
• Plot of genomes vs. of protein families

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MobileMotilityElement?
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Phylogenetic Distribution Novelty 1st Bacterial
Actin Related Protein
Haliangium ochraceum DSM 14365
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Phylogenetic Diversity Sequenced Bacteria
Archaea
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Phylogenetic Diversity with GEBA
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Phylogenetic Diversity Isolates
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Phylogenetic Diversity All
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• At least 40 phyla of bacteria
• Genome sequences are mostly from three phyla
• Most phyla with cultured species are sparsely
  sampled
• Lineages with no cultured taxa even more poorly
  sampled

Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Well sampled phyla
Poorly sampled
No cultured taxa
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Uncultured LineagesTechnical Approaches

• Get into culture
• Enrichment cultures
• If abundant in low diversity ecosystems
• Flow sorting
• Microbeads
• Microfluidic sorting
• Single cell amplification

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GEBA Lesson 6

• Need Experiments from Across the Tree of Life too

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As of 2002

• At least 40 phyla of bacteria

Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Based on Hugenholtz, 2002
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As of 2002

• At least 40 phyla of bacteria
• Experimental studies are mostly from three phyla

Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Based on Hugenholtz, 2002
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As of 2002

• At least 40 phyla of bacteria
• Experimental studies are mostly from three phyla
• Some studies in other phyla

Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Based on Hugenholtz, 2002
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As of 2002

• At least 40 phyla of bacteria
• Genome sequences are mostly from three phyla
• Some other phyla are only sparsely sampled
• Same trend in Eukaryotes

Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Based on Hugenholtz, 2002
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As of 2002

• At least 40 phyla of bacteria
• Genome sequences are mostly from three phyla
• Some other phyla are only sparsely sampled
• Same trend in Viruses

Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
Chloroflexi
Based on Hugenholtz, 2002
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Need experimental studies from across the tree too
Acidobacteria
Bacteroides
Fibrobacteres
Gemmimonas
Verrucomicrobia
Planctomycetes
0.1
Chloroflexi
Tree based on
Hugenholtz (2002)
with some
modifications.
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MICROBES
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A Happy Tree of Life
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GEBA Pilot Project Components

• Project overview (Phil Hugenholtz, Nikos
  Kyrpides, Jonathan Eisen)
• Project management (David Bruce, Lynne Goodwin et
  al)
• Culture collection and DNA prep (DSMZ,
  Hans-Peter Klenk)
• Libraries and DNA (Eileen Dalin et al)
• Sequencing and closure (Susan Lucas, Alla Lapidus
  et al.)
• Annotation and data release (Nikos Kyrpides)
• Analysis (Dongying Wu, Kostas Mavrommatis, Martin
  Wu, Jenna Morgan, Victor Kunin, Marcel Huntemann,
  Neil Rawlings, Ian Paulsen, Patrick Chain, Patrik
  DHaeseleer, Sean Hooper, Iain Anderson)
• Adopt a microbe education project (Cheryl
  Kerfeld)
• Outreach (David Gilbert)
• (DOE, Eddy Rubin, Jim Bristow)