Phylogenomics and the Diversity and Diversification of Microbes

Phylogenomics and the Diversity
and Diversification of Microbes

Jonathan A. Eisen
UC Davis

Calacademy Talk
December 16, 2010 1
Monday, November 26, 12

Phylogenomics of Novelty

Origin of New Genome
Functions and Dynamics
Processes
•Evolvability
•New genes •Repair and recombination
•Changes in old genes processes
•Changes in pathways •Intragenomic variation

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


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

3

Outline

• Introduction
• Phylogenomic Tales
– Selecting genomes for sequencing
– Species evolution
– Predicting functions of genes
– Uncultured microbes

4

Outline

• Introductino
• Phylogenomic Tales
– Selecting genomes for sequencing
– Species evolution
– Predicting functions of genes
– Uncultured microbes
• All of these going to be told in context of a
recent project “A Genomic Encyclopedia of
Bacteria and Archaea” (aka GEBA)
5

Fleischmann et al.
1995 6

Whole Genome Shotgun Sequencing

7


Warner Brothers, Inc.

7


shotgun


7


shotgun

sequence

7

Assemble Fragments

8

Assemble Fragments

sequencer output

8

Assemble Fragments

sequencer output

assemble
fragments

8

Assemble Fragments

sequencer output

assemble
fragments

Closure &

Annotation

8

From http://genomesonline.org 9

Human commensals

13

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
14

From http://genomesonline.org 15

rRNA Tree of Life
Bacteria

Archaea

Eukaryotes

FIgure from Barton, Eisen et al.
“Evolution”, CSHL Press.
Based on tree from Pace NR, 2003.


As of 2002 Proteobacteria
TM6
OS-K • At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Bacteroides bacteria
Chlorobi
Fibrobacteres
Marine GroupA
WS3
Gemmimonas
Firmicutes
Fusobacteria
Actinobacteria
OP9
Cyanobacteria
Synergistes
Deferribacteres
Chrysiogenetes
NKB19
Verrucomicrobia
Chlamydia
OP3
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermudesulfobacteria
Thermotogae
OP1 Based on
OP11 Hugenholtz, 2002 17

TM6
OS-K
• At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Chlorobi
Fibrobacteres
Marine GroupA • Genome
WS3
Gemmimonas
Firmicutes
sequences are
Fusobacteria
Actinobacteria
mostly from
OP9
Cyanobacteria
Synergistes
three phyla
Deferribacteres
Chrysiogenetes
NKB19
Verrucomicrobia
Chlamydia
OP3
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1 Based on

TM6
OS-K
• At least 40
Acidobacteria
Termite Group
OP8
phyla of
Nitrospira
Chlorobi
Fibrobacteres
WS3
Gemmimonas
Firmicutes
sequences are
Fusobacteria
Actinobacteria
mostly from
OP9
Cyanobacteria
Synergistes
three phyla
Deferribacteres
Chrysiogenetes
NKB19
• Some other
Verrucomicrobia
Chlamydia
OP3
phyla are
Planctomycetes
Spriochaetes only sparsely
Coprothmermobacter
OP10
Thermomicrobia
sampled
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1 Based on

Proteobacteria

2002 TM6
OS-K
Acidobacteria
• At least 40
Termite Group phyla of
OP8
Nitrospira
Bacteroides
bacteria
Chlorobi
Fibrobacteres
Marine GroupA
• Genome
WS3
Gemmimonas sequences are
Firmicutes
Fusobacteria mostly from
Actinobacteria
OP9 three phyla
Cyanobacteria
Synergistes
Deferribacteres
Chrysiogenetes
• Some other
NKB19
Verrucomicrobia phyla are only
Chlamydia
OP3
Planctomycetes
sparsely
Spriochaetes
Coprothmermobacter sampled
OP10
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1 Based on Hugenholtz,
OP11 2002

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

21

Proteobacteria
• NSF-funded TM6
OS-K
• At least 40
Tree of Life Acidobacteria
Termite Group phyla of
OP8
Project Nitrospira
Chlorobi
• A genome Fibrobacteres
WS3
from each of Gemmimonas sequences are
Firmicutes
eight phyla Fusobacteria
mostly from
Actinobacteria
OP9
Cyanobacteria
Synergistes
three phyla
Deferribacteres
Chrysiogenetes
NKB19
• Some other
Verrucomicrobia
Chlamydia
OP3
phyla are only
Planctomycetes
Spriochaetes sparsely
Coprothmermobacter
OP10
Thermomicrobia
sampled
Chloroﬂexi
TM7
Deinococcus-Thermus
• Solution I:
Dictyoglomus
Aquiﬁcae sequence more
Eisen & Ward, PIs Thermudesulfobacteria
Thermotogae
OP1 phyla
OP11 22

Organisms Selected
Phylum Species selected

Chrysiogenes Chrysiogenes arsenatis (GCA)

Coprothermobacter Coprothermobacter proteolyticus (GCBP)

Dictyoglomi Dictyoglomus thermophilum (GD T )

Thermodesulfobacteria Thermodesulfobacterium commune (GTC)

Nitrospirae Thermodesulfovibrio yellowstonii (GTY)

Thermomicrobia Thermomicrobium roseum (GTR )

Deferribacteres Geovibrio thiophilus (GGT)

Synergistes Synergistes jonesii (GSJ)
23

Bacterial aTOL Project AIMS

• Improve resolution of deep branches in the
bacterial tree

• Launch biological studies of these phyla

• Leverage data for interpreting
environmental surveys

24

Proteobacteria
• NSF-funded TM6
OS-K
• At least 40
Termite Group phyla of bacteria
OP8
Project Nitrospira
• Genome
Bacteroides

• A genome Chlorobi
Fibrobacteres sequences are
Marine GroupA
from each of WS3
Gemmimonas mostly from
eight phyla Firmicutes
Fusobacteria three phyla
Actinobacteria
OP9
Cyanobacteria
• Some other
Synergistes
Deferribacteres
Chrysiogenetes
phyla are only
NKB19
Verrucomicrobia sparsely
Chlamydia
OP3
Planctomycetes
sampled
Spriochaetes
Coprothmermobacter • Still highly
OP10
Thermomicrobia
Chloroﬂexi
biased in terms
TM7
Deinococcus-Thermus
Dictyoglomus
of the tree
Aquiﬁcae
Thermotogae
OP1
OP11


Major Lineages of Actinobacteria
2.5 Actinobacteria
2.5.1 Acidimicrobidae
2.5.1 Acidimicrobidae 2.5.1.1 Unclassified
2.5.1.2 "Microthrixineae
2.5.1.1 Unclassified 2.5.1.3 Acidimicrobineae
2.5.1.3.1 Unclassified
2.5.1.2 "Microthrixineae 2.5.1.3.2 Acidimicrobiaceae
2.5.1.4 BD2-10
2.5.1.3 Acidimicrobineae 2.5.1.5 EB1017
2.5.2 Actinobacteridae
2.5.1.4 BD2-10 2.5.2.1 Unclassified
2.5.2.10 Ellin306/WR160
2.5.1.5 EB1017 2.5.2.11 Ellin5012
2.5.2.12 Ellin5034
2.5.2 Actinobacteridae 2.5.2.13 Frankineae
2.5.2.1 Unclassified 2.5.2.13.2 Acidothermaceae

2.5.2.10 Ellin306/WR160 2.5.2.13.3
2.5.2.13.4
Ellin6090
Frankiaceae

2.5.2.11 Ellin5012 2.5.2.13.5
2.5.2.13.6
Geodermatophilaceae
Microsphaeraceae

2.5.2.12 Ellin5034 2.5.2.13.7
2.5.2.14
Sporichthyaceae
Glycomyces
2.5.2.13 Frankineae 2.5.2.15
2.5.2.15.1
Intrasporangiaceae
Unclassified
2.5.2.14 Glycomyces 2.5.2.15.2
2.5.2.15.3
Dermacoccus
Intrasporangiaceae
2.5.2.15 Intrasporangiaceae 2.5.2.16
2.5.2.17
Kineosporiaceae
Microbacteriaceae
2.5.2.16 Kineosporiaceae 2.5.2.17.1
2.5.2.17.2
Unclassified
Agrococcus
2.5.2.17 Microbacteriaceae 2.5.2.17.3
2.5.2.18
Agromyces
Micrococcaceae
2.5.2.18 Micrococcaceae 2.5.2.19
2.5.2.2
Micromonosporaceae
Actinomyces
2.5.2.19 Micromonosporaceae 2.5.2.20
2.5.2.20.1
Propionibacterineae
Unclassified
2.5.2.2 Actinomyces 2.5.2.20.2
2.5.2.20.3
Kribbella
Nocardioidaceae
2.5.2.20 Propionibacterineae 2.5.2.20.4
2.5.2.21
Propionibacteriaceae
Pseudonocardiaceae
2.5.2.21 Pseudonocardiaceae 2.5.2.22
2.5.2.22.1
Streptomycineae
Unclassified
2.5.2.22 Streptomycineae 2.5.2.22.2
2.5.2.22.3
Kitasatospora
Streptacidiphilus
2.5.2.23 Streptosporangineae 2.5.2.23
2.5.2.23.1
Streptosporangineae
Unclassified
2.5.2.3 Actinomycineae 2.5.2.23.2
2.5.2.23.3
Ellin5129
Nocardiopsaceae
2.5.2.4 Actinosynnemataceae 2.5.2.23.4
2.5.2.23.5
Streptosporangiaceae
Thermomonosporaceae
2.5.2.5 Bifidobacteriaceae 2.5.2.3 Actinomycineae
2.5.2.4 Actinosynnemataceae
2.5.2.6 Brevibacteriaceae 2.5.2.5 Bifidobacteriaceae
2.5.2.6 Brevibacteriaceae
2.5.2.7 Cellulomonadaceae 2.5.2.7 Cellulomonadaceae
2.5.2.8 Corynebacterineae
2.5.2.8 Corynebacterineae 2.5.2.8.1 Unclassified
2.5.2.8.2 Corynebacteriaceae
2.5.2.9 Dermabacteraceae 2.5.2.8.3 Dietziaceae
2.5.2.8.4 Gordoniaceae
2.5.3 Coriobacteridae 2.5.2.8.5 Mycobacteriaceae
2.5.2.8.6 Rhodococcus
2.5.3.1 Unclassified 2.5.2.8.7 Rhodococcus
2.5.2.8.8 Rhodococcus
2.5.3.2 Atopobiales 2.5.2.9 Dermabacteraceae
2.5.3.3 Coriobacteriales 2.5.2.9.2 Brachybacterium
2.5.2.9.3 Dermabacter
2.5.3.4 Eggerthellales 2.5.3 Coriobacteridae
2.5.3.1 Unclassified
2.5.4 OPB41 2.5.3.2 Atopobiales
2.5.3.3 Coriobacteriales
2.5.5 PK1 2.5.3.4 Eggerthellales
2.5.4 OPB41
2.5.6 Rubrobacteridae 2.5.5 PK1
2.5.6 Rubrobacteridae
2.5.6.1 Unclassified 2.5.6.1 Unclassified
2.5.6.2 "Thermoleiphilaceae
2.5.6.2 "Thermoleiphilaceae 2.5.6.2.1 Unclassified

27
2.5.6.2.2 Conexibacter
2.5.6.3 MC47 2.5.6.2.3 XGE514
2.5.6.3 MC47
2.5.6.4 Rubrobacteraceae 2.5.6.4 Rubrobacteraceae


Proteobacteria
• NSF-funded TM6
OS-K
• At least 40
OP8
Project Nitrospira
• Genome
Bacteroides

Marine GroupA
from each of WS3
Actinobacteria
OP9
Cyanobacteria
• Some other
Synergistes
Deferribacteres
Chrysiogenetes
phyla are only
NKB19
Chlamydia
OP3
Planctomycetes
sampled
Spriochaetes
Coprothmermobacter • Same trend in
OP10
Thermomicrobia
Chloroﬂexi
Archaea
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1
OP11


Proteobacteria
• NSF-funded TM6
OS-K
• At least 40
OP8
Project Nitrospira
• Genome
Bacteroides

Marine GroupA
from each of WS3
Actinobacteria
OP9
Cyanobacteria
• Some other
Synergistes
Deferribacteres
Chrysiogenetes
phyla are only
NKB19
Chlamydia
OP3
Planctomycetes
sampled
Spriochaetes
OP10
Thermomicrobia
Chloroﬂexi
Eukaryotes
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1
OP11


Proteobacteria
• NSF-funded TM6
OS-K
• At least 40
OP8
Project Nitrospira
• Genome
Bacteroides

Marine GroupA
from each of WS3
Actinobacteria
OP9
Cyanobacteria
• Some other
Synergistes
Deferribacteres
Chrysiogenetes
phyla are only
NKB19
Chlamydia
OP3
Planctomycetes
sampled
Spriochaetes
OP10
Thermomicrobia
Chloroﬂexi
Viruses
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1
OP11


Proteobacteria
• GEBA TM6
OS-K • At least 40
Acidobacteria
• A genomic Termite Group
OP8
phyla of bacteria
encyclopedia Nitrospira
Bacteroides • Genome
Chlorobi
of bacteria Fibrobacteres
Marine GroupA
sequences are
and archaea WS3
Firmicutes
Actinobacteria
OP9
Cyanobacteria • Some other
Synergistes
Deferribacteres
Chrysiogenetes
phyla are only
NKB19
Chlamydia
OP3
Planctomycetes
sampled
Spriochaetes
Coprothmermobacter
OP10
• Solution: Really
Thermomicrobia
Chloroﬂexi Fill in the Tree
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Eisen & Ward, PIs Thermotogae
OP1
OP11


http://www.jgi.doe.gov/programs/GEBA/pilot.html 32

GEBA Pilot Project Overview
• Identify major branches in rRNA tree for
which no genomes are available
• Identify those with a cultured representative in
DSMZ
• DSMZ grew > 200 of these and prepped DNA
• Sequence and ﬁnish 100+ (covering breadth of
bacterial/archaea diversity)
• Annotate, analyze, release data
• Assess beneﬁts of tree guided sequencing
• 1st paper Wu et al in Nature Dec 2009

GEBA Pilot Project: Components
• Project overview (Phil Hugenholtz, Nikos Kyrpides, Jonathan
Eisen, Eddy Rubin, Jim Bristow)
• Project management (David Bruce, Eileen Dalin, Lynne Goodwin)
• Culture collection and DNA prep (DSMZ, Hans-Peter Klenk)
• Sequencing and closure (Eileen Dalin, Susan Lucas, Alla Lapidus,
Mat Nolan, Alex Copeland, Cliff Han, Feng Chen, Jan-Fang Cheng)
• Annotation and data release (Nikos Kyrpides, Victor Markowitz, et
al)
• Analysis (Dongying Wu, Kostas Mavrommatis, Martin Wu, Victor
Kunin, Neil Rawlings, Ian Paulsen, Patrick Chain, Patrik
D’Haeseleer, Sean Hooper, Iain Anderson, Amrita Pati, Natalia N.
Ivanova, Athanasios Lykidis, Adam Zemla)
• Adopt a microbe education project (Cheryl Kerfeld)
• Outreach (David Gilbert)
• $$$ (DOE, Eddy Rubin, Jim Bristow)
34

GEBA Phylogenomic Lesson 1

The rRNA Tree of Life is a Useful Tool
for Identifying Phylogenetically Novel
Genomes

35

Network of Life
Bacteria

Archaea

Eukaryotes

Figure from Barton, Eisen et al.


“Whole Genome” Concatenation Tree
w/ AMPHORA

See Wu and Eisen, Genome Biology 2008 9: R151
http://bobcat.genomecenter.ucdavis.edu/AMPHORA/

Compare PD in Trees


PD of rRNA, Genome Trees Similar

From Wu et al. 2009 Nature 462, 1056-1060



rRNA Tree is good but not perfect
and better genomic sampling improves
phylogenetic inference

42

16s Says Hyphomonas is in Rhodobacteriales

Badger et al.
2005
43

WGT and individual gene trees:
Its Related to Caulobacterales

Badger et al.
2005
44


Phylogeny-driven genome selection
helps discover new genetic diversity


Network of Life
Bacteria

Archaea

Eukaryotes

FIgure from Barton, Eisen et al.


Protein Family Rarefaction Curves

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


Synapomorphies exist


Structural Novelty

• Of the 17000 protein families in the GEBA56, 1800
are novel in sequence (Wu)

• Structural modeling suggests many are structurally
novel too (D'haeseleer)

• 372 being crystallized by the PSI (Kerfeld)


Phylogenetic Distribution Novelty:
Bacterial Actin Related Protein
C. boidinii gi57157304
S. cerevisiae gi14318479
L. starkeyi gi166080363
S. japonicus gi213407080 ACTIN
A. cliftonii gi14269497
99 U. pertusa gi50355609
H. sapiens gi4501889
M. cerebralis gi46326807
67 C. cinerea gi169844021
N. crassa gi85101929 ARP1
100 I. scapularis gi215507378
51 100 H. sapiens gi5031569
65 S. japonicus gi213404844
100 S. cerevisiae gi6320175
ARP2
D. melanogaster gi24642545
100 G. gallus gi45382569
75 C. neoformans gi58266690
S. cerevisiae gi6322525 ARP3
100 D. melanogaster gi17737543
100 H. sapiens gi5031573
H. ochraceum gi227395998 BARP
S. cerevisiae gi1008244
73 P. patens gi168051992 ARP4
99 A. thaliana gi18394608
100 S. japonicus gi213408393 ARP5
87 D. discoideum gi66802418
74 D. melanogaster gi17737347
100 D. hansenii gi21851 1921 ARP6
100 O. sativa gi182657420
A. thaliana gi1841 1737 ARP7
D. melanogater gi19920358
100 M. musculus gi226246593 ARP10

0.5

Haliangium ochraceum DSM 14365 Patrik D’haeseleer, Adam Zemla,
Victor Kunin
See also Guljamow et al. 2007 Current Biology.


Phylogeny driven genome selection
(and phylogenetics in general)
improves genome annotation

52

Predicting Function

• Key step in genome projects
• More accurate predictions help guide
experimental and computational analyses
• Many diverse approaches
• All improved both by “phylogenomic” type
analyses that integrate evolutionary
reconstructions and understanding of how
new functions evolve

53

Most/All Functional Prediction Improves
w/ Better Phylogenetic Sampling
• Took 56 GEBA genomes and compared results vs. 56
randomly sampled new genomes
• 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
Kostas Natalia Thanos Nikos Iain
Mavrommatis Ivanova Lykidis Kyrpides Anderson



Metadata and individual genome
papers important

55

SIGS
http://standardsingenomics.org/

56


Improves analysis of genome data
from uncultured organisms

57

Great Plate Count Anomaly

Culturing Microscope

Count Count

58



Count <<<< Count

59


DNA


Count <<<< Count

60

PCR Saves the Day

61

rRNA Phylotyping
• Collect DNA from
environment
• PCR amplify rRNA
genes using broad (so-
called universal) primers
• Sequence
• Align to others
• Infer evolutionary tree
• Unknowns “identiﬁed”
by placement on tree
• Some use BLAST, but
not as good as phylogeny
62

Uses of rRNA sequences

The Hidden Majority Richness estimates

Hugenholtz 2002 Bohannan and
Hughes 2003
63

rRNA: A Phylogenetic Anchor to
Determine Who’s Out There

Eisen et
al. 1992
64

rRNA: A Phylogenetic Anchor to
Determine Who’s Out There

Biology not Eisen et
similar enough al. 1992
64

Metagenomics

shotgun

clone


Example I: Phylotyping with
rRNA and other genes

67

Weighted % of Clones

0
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0.2500
0.3750
0.5000
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Major Phylogenetic Group
Sargasso Phylotypes

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Shotgun Sequencing Allows Use of Other Markers

Venter et al., 2004
68
EFG
EFTu

rRNA
RecA
RpoB
HSP70


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Venter et al., 2004
69
EFG
EFTu

rRNA
RecA
RpoB
HSP70

Example II: Binning

70

Metagenomics Challenge


Binning challenge

A T
B U
C V
D W
E X
F Y
G Z
72

Glassy Winged Sharpshooter

• Feeds on xylem
sap
• Vector for
Pierce’s Disease
• Potential
bioterror agent

73

Xylem and Phloem

From
Lodish et
al. 2000

74

Wu et al. 2006 PLoS Biology 4: e188. 75

Sharpshooter Shotgun Sequencing

shotgun

Collaboration with Nancy
Moran’s lab

Baumannia is a Vitamin and
Cofactor Producing Machine

Wu et al.
2006
PLoS
Biology 4:
e188. 77

No Amino-Acid Synthesis

78

???????

80

Commonly Used Binning Methods
Did not Work Well

• Assembly
– Only Baumannia generated good contigs
• Depth of coverage
– Everything else 0-1X coverage
• Nucleotide composition
– No detectible peaks in any vector we looked at

81

CFB Phyla

82

Essential Amino Acid Synthesis

Wu et al. 2006 PLoS
Biology 4: e188. 84

Sulcia makes amino acids

Baumannia makes vitamins and cofactors



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Sargasso Phylotypes

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Cannot be done

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or
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iro
ch
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te
Fu
so s
De ba
in ct
er
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sampling of genomes

oc
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ry r
ar mu
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ae
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ta

Venter et al., 2004
87
EFG
EFTu

rRNA
RecA
RpoB
HSP70

Phylogenomics and the Diversity and Diversification of Microbes

Phylogenomics and the Diversity and Diversification of Microbes

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