Towards a Field Guide to the Microbes for #AAASMtg

Towards A Field Guide to the Microbes

Jonathan A. EisenUniversity of California, Davis

Twitter: @phylogenomics

AAAS Annual Meeting 2012February 17, 2012

Saturday, February 18, 12

Embargoes

• Note - slides will be posted to slideshare• Post anything about this you want• Discuss, blog, tweet, critique, mock,

whatever• Just don’t keep it secret


I. The Story of a Bird


4


4





8


9


Robin in London Examples



MICROBES


MICROBES


II. More on Field Guides


What is a Field Guide?

• Takes knowledge about taxonomy & diversity of organisms (or other entities) and converts it into a simple, portable, representation.

• Covers ranges, niches, phenotypes, genetics, means of identification, etc.

• Can include a checklist.• Used by amateurs & professionals.


Diversity of Guild Guides

from Diane Schmidt at http://www.library.illinois.edu/bix/fieldguides/index.html


http://www.library.illinois.edu/bix/fieldguides/index.html













A Field Guide to Bacteria

http://www.amazon.com/Field-Guide-Bacteria-Comstock-Book/dp/0801488540






Other Microbial Field Guides


What is a Field Guide?

• Takes knowledge about taxonomy & diversity of organisms (or other entities) and converts it into a simple, portable, representation.

• Covers ranges, niches, phenotypes, genetics, means of identification, etc.

• Can include a checklist.• Used by amateurs & professionals.


What is needed?

• Catalog of types of organisms• Biogeography (space & time); ranges• Niche information• Phenotypes and functions• Genetic diversity• Means for identification• Amateur participation


What is needed?



How many species?


Culturing Microbes


Culturing Microbes


Culturing Microbes


Mendeley Group

http://www.mendeley.com/groups/1359493/number-of-species-of-bacteria-and-archaea/




Cataloguing Types w/ DNA

• rRNA surveys• metagenomics • other metaomics

• Key issues• Phylogenetic classification• Reference data limited outside of rRNA• Phylogenetic diversity vs. OTUs• What is a species/OTU?


Metagenomic Phylotpying

rRNA Phylotyping in Sargasso Sea Metagenomic

Metagenomic Data

Venter et al., Science 304: 66. 2004


http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15001713&query_hl=2




Metagenomic Phylotyping

0

0.1250

0.2500

0.3750

0.5000

Alphapro

teobacteria

Betap

roteobacteria

Gamm

aproteobacteria

Epsilo

nproteobacteria

Deltapro

teobacteria

Cyanobacteria

Firmicutes

Actinobacteria

ChlorobiCFB

Chloroflexi

Spirochaetes

Fusobacteria

Deinococcus-Th

ermus

Euryarchaeota

Crenarchaeota

Sargasso Phylotypes

Wei

ghte

d %

of C

lone

s

Major Phylogenetic Group

EFGEFTuHSP70RecARpoBrRNA

Venter et al., Science 304: 66. 2004






AMPHORA

Wu and Eisen Genome Biology 2008 9:R151 doi:10.1186/gb-2008-9-10-r151




RecAGOS 1

GOS 2

GOS 3

GOS 4

GOS 5

RecA

Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, et al. (2011) Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees. PLoS ONE 6(3): e18011. doi:10.1371/journal.pone.0018011

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018011Saturday, February 18, 12

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018011

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018011

RpoB Too


What is needed?



What is needed?

• Catalog of types of organisms• EMP• Niche information• Phenotypes and functions• Genetic diversity• Means for identification• Amateur participation


What is needed?



What is needed?

• Catalog of types of organisms• Biogeography (space & time); ranges• METADATA• Phenotypes and functions• Genetic diversity• Means for identification• Amateur participation


What is needed?



Phylogenetic Diversity

• Phylogenetic diversity poorly sampled

• GEBA project at DOE-JGI correcting this


AMPHORA ALL

Kembel et al. PLoS One 2011





New Markers

Dongying Wu et al. in prep

Phylogenetic group Genome Number Gene Number Maker Candidates

Archaea 62 145415 106

Actinobacteria 63 267783 136

Alphaproteobacteria 94 347287 121

Betaproteobacteria 56 266362 311

Gammaproteobacteria 126 483632 118

Deltaproteobacteria 25 102115 206

Epislonproteobacteria 18 33416 455

Bacteriodes 25 71531 286

Chlamydae 13 13823 560

Chloroflexi 10 33577 323

Cyanobacteria 36 124080 590

Firmicutes 106 312309 87

Spirochaetes 18 38832 176

Thermi 5 14160 974

Thermotogae 9 17037 684


Phylosift

• New version of Amphora• Developed by Aaron Darling, Holly Bik,

Erick Matsen, Guillaume Jospin, Dongying Wu, et al.

• http://phylosift.wordpress.com/tag/github/• Supported by DHS, etc.• Will work for more markers, viruses,

eukaryotes ...


Major phyla of bacteria & archaea

No cultures

Some cultures


GEBA Uncultured

46

Number of SAGs from Candidate Phyla

OD

1

OP

11

OP

3

SA

R4

06

Site A: Hydrothermal vent 4 1 - -Site B: Gold Mine 6 13 2 -Site C: Tropical gyres (Mesopelagic) - - - 2Site D: Tropical gyres (Photic zone) 1 - - -

Sample collections at 4 additional sites are underway.

Phil Hugenholtz


No cultures

Some cultures

Functional Diversity?


What is needed?



Citizen Microbiology

http://www.microbe.net/citizen-science-projects/CITIZENMICROBIOLOGY.ORG


http://www.microbe.net/citizen-science-projects/

http://www.microbe.net/citizen-science-projects/

What is needed?

• Catalog of types of organisms• Biogeography (space & time); ranges• Niche information• Phenotypes and functions• Genetic diversity• Means for identification• Amateur participation• BONUS: Openness


What is needed?

• Open publications• Open data• Open tools• Open discussion

http://www.openmicrobiome.org/


http://www.openmicrobiome.org

http://www.openmicrobiome.org

Plant/Animal Field Studies














Microbial Field Studies















MICROBES


Acknowledgements

• $$$• DOE• NSF• GBMF• Sloan• DARPA

• People, places• DOE JGI: Eddy Rubin, Phil Hugenholtz et al.• UC Davis: Aaron Darling, Dongying Wu• Other: Jessica Green, Katie Pollard, Martin Wu,

Tom Slezak, Jack Gilbert


Towards a Field Guide to the Microbes for #AAASMtg

Technology

functions genetic diversity

catalog of types

rrna phylogenetic diversity

culturing microbessaturday

field guideto

reca reca gos

microbial field guidessaturday

amphora wu