Jonathan Eisen slides for #HMP2010

A phylogeny driven genomic
encyclopedia of bacteria and
archaea

Jonathan A. Eisen
UC Davis

Talk for HMP2010
September 2, 2010

Progress in Genome Sequencing

From http://genomesonline.org

Way Back Machine - 2002

454

Illumina

Way Back Machine - 2002

454

Illumina

Solid

Proteobacteria

2002 TM6
OS-K
Acidobacteria
• At least 40
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 Hugenholtz,
OP11 2002

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

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

Why Increase Phylogenetic Coverage?
• Common approach within some eukaryotic
groups (FGP, NHGRI, etc)
• Many successful small projects to ﬁll in
bacterial or archaeal gaps
• Phylogenetic gaps in bacterial and archaeal
projects commonly lamented in literature
• Many potential beneﬁts

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

Proteobacteria
OS-K
OP8
Project Nitrospira
• Genome
Bacteroides
Chlorobi
Marine GroupA
sequences are
from each of WS3
Actinobacteria
OP9
Cyanobacteria
Synergistes
• Some other
Deferribacteres
NKB19
Verrucomicrobia
Chlamydia
sparsely sampled
OP3
Planctomycetes
Spriochaetes
• Still highly
Coprothmermobacter
OP10 biased in terms
Thermomicrobia
Chloroﬂexi
TM7
of the tree
Deinococcus-Thermus
Dictyoglomus
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
2.5.2.13.3 Ellin6090
2.5.2.10 Ellin306/WR160 2.5.2.13.4 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
2.5.2.4
Actinomycineae
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
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
OS-K
OP8
Project Nitrospira
• Genome
Bacteroides
Chlorobi
Marine GroupA
sequences are
from each of WS3
Actinobacteria
OP9
Cyanobacteria
Synergistes
• Some other
Deferribacteres
NKB19
Verrucomicrobia
Chlamydia
sparsely sampled
OP3
Planctomycetes
Spriochaetes
• Same trend in
Coprothmermobacter
OP10 Archaea
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1
OP11

Proteobacteria
OS-K
OP8
Project Nitrospira
• Genome
Bacteroides
Chlorobi
Marine GroupA
sequences are
from each of WS3
Actinobacteria
OP9
Cyanobacteria
Synergistes
• Some other
Deferribacteres
NKB19
Verrucomicrobia
Chlamydia
sparsely sampled
OP3
Planctomycetes
Spriochaetes
• Same trend in
Coprothmermobacter
OP10 Eukaryotes
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1
OP11

Proteobacteria
OS-K
OP8
Project Nitrospira
• Genome
Bacteroides
Chlorobi
Marine GroupA
sequences are
from each of WS3
Actinobacteria
OP9
Cyanobacteria
Synergistes
• Some other
Deferribacteres
NKB19
Verrucomicrobia
Chlamydia
sparsely sampled
OP3
Planctomycetes
Spriochaetes
• Same trend in
Coprothmermobacter
OP10 Viruses
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Thermotogae
OP1
OP11

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

GEBA Pilot Project Overview
• Identify major branches in rRNA tree for
which no genomes are available
• Identify branches 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, DSMZ, GBMF)

GEBA Lesson 1

rRNA Tree is Useful for Identifying
Phylogenetically Novel Organisms

rRNA Tree of Life
Bacteria

Archaea

Eukaryotes

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

Network of Life
Bacteria

Archaea

Eukaryotes

Figure from Barton, Eisen et al.

“Whole Genome” Tree w/ AMPHORA

http://itol.embl.de/

Analogous to method of Ciccarelli et al.

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

PD of rRNA, Genome Trees Similar

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

GEBA Lesson 2

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

Phylogenetic Distribution Novelty:
Bacterial Actin Related Protein
2"#3)&4&*&& !"#*)$*),+%
5"#$-.-6&0&1- !"#$%,$-%)(
7"#0(1.8-9& !"#$''+-+,',!
5"#:1,)*&$/0 !"#&$,%+)+-+ !"#$%
!"#$%&'()*&& !"#$%&'(%()
(( +"#,-.(/01 !"#*+,**'+(
;"#01,&-*0 !"#%*+$--(
<"#$-.-3.1%&0 !"#%',&'-+)
') 2"#$&*-.-1 !"#$'(-%%+&$
="#$.1001 !"#-*$+$(&( !&'(
$++ >"#0$1,/%1.&0 !"#&$**+),)-!
*$ $++ ;"#01,&-*0 !"#*+,$*'(
'* 5"#:1,)*&$/0 !"#&$,%+%-%%
$++ 5"#$-.-6&0&1- !"#',&+$)*
!&')
?"#@-%1*)A10(-. !"#&%'%&*%*
$++ B"#A1%%/0# "#%*,-&*'(
)* 2"#*-)').@1*0 !"#*-&'''(+
5"#$-.-6&0&1- !"#',&&*&* !&'*
$++ ?"#@-%1*)A10(-. !"#$)),)*%,
$++ ;"#01,&-*0 !"#*+,$*),!
;"#)$C.1$-/@ !"#&&),(*((- +!&'
5"#$-.-6&0&1- !"#$++-&%%!
), ."#,1(-*0 !"#$'-+*$((&! !&',
(( !"#(C1%&1*1 !"#$-,(%'+-!
(% 5"#$-.-6&0&1- !"#$,+$(,&
$++ 5"#:1,)*&$/0 !"#&$,%+-,(,! !&'-
-) ?"#4&0$)&4-/@ !"#''-+&%$-
)% ?"#@-%1*)A10(-. !"#$)),),%)
() 5"#$-.-6&0&1- !"#',&,$$%
$++ ?"#C1*0-*&&!"#&$-*$ $(&$ !&'.
$++ D"#01(&61 !"#$-&'*)%&+!
!"#(C1%&1*1!"#$-%$ $),) !&'/
?"#@-%1*)A1(-. !"#$((&+,*-
$++ <"#@/0$/%/0 !"#&&'&%'*(, !&'(0

+/*!

Haliangium ochraceum DSM 14365 Patrik D’haeseleer, Adam Zemla,
Victor Kunin

See also Guljamow et al. 2007 Current Biology.

GEBA Lesson 3

improves genome annotation

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

Kostas Natalia Thanos Nikos Iain
Mavrommatis Ivanova Lykidis Kyrpides Anderson

GEBA Lesson 4

Metadata and individual genome
papers important

SIGS
http://standardsingenomics.org/

GEBA Lesson 5

improves analysis of metagenome data

rRNA phylotyping from metagenomics

Venter et al., 2004

Shotgun Sequencing Allows Use of
Alternative Anchors (e.g., RecA)

Venter et al., 2004

Weighted % of Clones

0
0.1250
0.2500
0.3750
0.5000
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Shotgun Sequencing Allows Use of Other Markers

Venter et al., 2004
EFG
EFTu

rRNA
RecA
RpoB
HSP70

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

Binning challenge
A T
B U
C V
D W
E X
F Y
G Best binning method: reference genomes Z

Reference Genomes Coming from
Select Environment

Binning challenge
A T
B U
C V
D W
E X
F Y
G No reference genome? What do you do? Z

Binning challenge
A T
B U
C V
D W
E X
F Y
G No reference genome? What do you do? Z
Phylogeny ....

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AMPHORA - each read on its own tree
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Phylogenetic Binning Using AMPHORA
frr

tsf
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rplF

rplP

rplT
rplE
infC

rpsI
rplS
rplA
rplB

rplK
rplC

rpsJ
rplN
rplD

rplM

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rpsK
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Metagenomic Analysis Improves
w/ Phylogenetic Sampling
• Small but real improvements in
–Gene identification / confirmation
–Functional prediction
–Binning
–Phylogenetic classification

Metagenomic Analysis Improves
w/ Phylogenetic Sampling
• Small but real improvements in
–Gene identification / confirmation
–Functional prediction
–Binning
–Phylogenetic classification
• But not a lot ...

GEBA Future 1

Need to adapt genomic and
metagenomic methods to make use of
GEBA data

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Improving Phylogeny for
Metagenomic Reads
• Examples using reference trees
– AMPHORA (Wu and Eisen)
– PPlacer (Erik Matsen)
– FastTree (Morgan Price)
• Variants
– Use concatenated alignment of markers not just
individual genes (Steven Kembel)
– Apply to OTU identiﬁcation not just classiﬁcation
(Thomas Sharpton)
– CoBinning: look for linkage among fragments/genes
(Aaron Darling)

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Pr ac
ot te
eo ria
ba
Cy ct
an er
ob ia
ac
Ch te
ria
la
m
Ac yd
id ia
ob e
Ba act
ct er
er ia
Ac oi
de
tin te
ob s
ac
gene families

te
ria
Aq
Pl ui
an fic
ct
om ae
yc
Sp et

iro es
ch
ae
Fi te
rm s
ic
ut
Improves with more

Ch es
lo
ro
U fle
nc xi
la Ch
ss lo
ifi ro
ed bi
Ba
ct
er
ia
frr

tsf
pgk

rplL
rplF

rplP

rplT
rplE
infC

rpsI
rplS
rplA
rplB

rplK
rplC

rpsJ
rplN
rplD

rplM

rpsE

rpsS
rpsB

rpsK
rpsC
rpoB

rpsM
pyrG
nusA
dnaG

rpmA

smpB

Keep only the families with:

Universality * Evenness * monophyly >= 90*90*90

Phylogenetic group Genome Number Gene Number Maker Candidates

Archaea 62 145415 102

Actinobacteria 63 267783 136

Alphaproteobacteria 94 347287 142

Betaproteobacteria 56 266362 294

Gammaproteobacteria 126 483632 141

Deltaproteobacteria 25 102115 44

Epislonproteobacteria 18 33416 446

Bacteriodes 25 71531 179

Chlamydae 13 13823 561

Chloroflexi 10 33577 140

Cyanobacteria 36 124080 532

Firmicutes 106 312309 80

Spirochaetes 18 38832 72

Thermi 5 14160 727

Thermotogae 9 17037 646

Al
ph
ap
ro
Be te
ta ob
G

0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
pr ac
am ot te
m eo ria
ap ba
ro ct
D te er
el ob ia
ta
pr ac
Ep ot te
U si
lo eo ria
nc ba
la np
ss ro ct
ifi te er
ed ob ia
Pr ac
ot te
eo ria
ba
Cy ct
an er
ob ia
ac

Ac
Ch
la
m
te

yd
ria models
id ia
ob e
Ba act
ct er
er ia
Ac oi
de
tin te
ob s
ac
te
ria
Aq
Improves with

Pl ui
an fic
ct
om ae
yc
Sp et

iro es
ch
ae
Fi te
rm s
ic
ut
Ch es
lo
ro
U fle
nc xi
la Ch
ss
rebuilding gene family

ifi lo
ed ro
bi
Ba
ct
er
ia
frr

tsf
pgk

rplL
rplF

rplP

rplT
rplE
infC

rpsI
rplS
rplA
rplB

rplK
rplC

rpsJ
rplN
rplD

rplM

rpsE

rpsS
rpsB

rpsK
rpsC
rpoB

rpsM
pyrG
nusA
dnaG

rpmA

smpB

Other Ways to Make Better Use
of the Data
• Rebuild protein family models
• Experiments from across the tree needed
• Need better phylogenies, including HGT
• Improved tools for using distantly related
genomes in metagenomic analysis
• Better recording and sharing of metadata
about organisms

GEBA Future 2

The dark matter of the biological
universe

Phylogenetic Diversity:
Sequenced Bacteria & Archaea

From Wu et al. 2009

Phylogenetic Diversity with
GEBA

From Wu et al. 2009

Phylogenetic Diversity: Isolates

From Wu et al. 2009

Phylogenetic Diversity: All

From Wu et al. 2009

Proteobacteria
TM6
OS-K
• At least 40 phyla of bacteria
Acidobacteria
Termite Group
OP8
• Genome sequences are mostly
Nitrospira
Bacteroides from three phyla
Chlorobi
Fibrobacteres
Marine GroupA • Most phyla with cultured
WS3
Gemmimonas
Firmicutes
species are sparsely sampled
Fusobacteria
Actinobacteria • Lineages with no cultured
OP9
Cyanobacteria
Synergistes
taxa even more poorly
Deferribacteres
Chrysiogenetes
NKB19
sampled
Verrucomicrobia
Chlamydia
OP3
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Well sampled phyla
Thermotogae Poorly sampled
OP1
OP11 No cultured taxa

Proteobacteria
TM6
OS-K
Acidobacteria
Termite Group
• At least 40 phyla of bacteria
OP8
Nitrospira • Genome sequences are mostly
Bacteroides
Chlorobi
Fibrobacteres
from three phyla
Marine GroupA
WS3 • Most phyla with cultured
Gemmimonas
Firmicutes species are sparsely sampled
Fusobacteria
Actinobacteria
OP9
• Lineages with no cultured taxa
Cyanobacteria
Synergistes even more poorly sampled
Deferribacteres
Chrysiogenetes
NKB19
Verrucomicrobia
Chlamydia
OP3
Planctomycetes
Spriochaetes
Coprothmermobacter
OP10
Thermomicrobia
Chloroﬂexi
TM7
Deinococcus-Thermus
Dictyoglomus
Aquiﬁcae
Well sampled phyla
Thermotogae Poorly sampled
OP1
OP11 No cultured taxa

Uncultured Lineages:
Technical Approaches
• Get into culture
• Enrichment cultures
• If abundant in low diversity ecosystems
• Flow sorting
• Microbeads
• Microﬂuidic sorting
• Single cell ampliﬁcation

Jonathan Eisen slides for #HMP2010

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Jonathan Eisen slides for #HMP2010

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