Towards a Field Guide to the Microbes for #AAASMtg

Towards A Field Guide to the Microbes Jonathan A. Eisen University of California, Davis Twitter: @phylogenomics AAAS Annual Meeting 2012 February 17, 2012Saturday, 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 secretSaturday, February 18, 12

I. The Story of a BirdSaturday, February 18, 12

4Saturday, February 18, 12

Saturday, February 18, 12

Robin in London ExamplesSaturday, February 18, 12

MICROBESSaturday, February 18, 12

II. More on Field GuidesSaturday, February 18, 12

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.Saturday, February 18, 12

Diversity of Guild Guides from Diane Schmidt at http://www.library.illinois.edu/bix/ﬁeldguides/index.htmlSaturday, February 18, 12

A Field Guide to Bacteria http://www.amazon.com/Field-Guide- Bacteria-Comstock-Book/dp/0801488540Saturday, February 18, 12

Other Microbial Field GuidesSaturday, February 18, 12

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.Saturday, February 18, 12

What is needed? • Catalog of types of organisms • Biogeography (space & time); ranges • Niche information • Phenotypes and functions • Genetic diversity • Means for identification • Amateur participationSaturday, February 18, 12

How many species?Saturday, February 18, 12

Culturing MicrobesSaturday, February 18, 12

Mendeley Group http://www.mendeley.com/groups/1359493/number-of-species-of-bacteria-and-archaea/Saturday, February 18, 12

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?Saturday, February 18, 12

Metagenomic Phylotpying rRNA Phylotyping in Sargasso Sea Metagenomic Metagenomic Data Venter et al., Science 304: 66. 2004Saturday, February 18, 12

Saturday, February 18, 12 Weighted % of Clones 0 0.1250 0.2500 0.3750 0.5000 Al ph ap ro Be ta et G pr oba ot am eo cte m ba ria Ep ap ct si rot er lo ia np eob De ro ac lta te te pr ob ria o a EFG EFTu C teo cte rRNA RecA RpoB ya b ria HSP70 no ac b te Fi act ria rm er Ac ic ia tin ut es ob a C cte hl ri or a ob C i FB C hl o Major Phylogenetic Group Sp rofl Sargasso Phylotypes iro ex i 304: 66. 2004 ch Metagenomic Phylotyping Fu a De so ete in ba s oc ct oc er cu ia Venter et al., Science Eu s ry -Th a e C rch rm re a na eous rc t ha a eo ta

AMPHORA Wu and Eisen Genome Biology 2008 9:R151 doi: 10.1186/ gb-2008-9-10- r151Saturday, February 18, 12

Wu and Eisen Genome Biology 2008 9:R151 doi:10.1186/gb-2008-9-10-r151Saturday, February 18, 12

GOS 1 GOS 2 RecA RecA GOS 3 GOS 4 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. GOS 5 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

RpoB TooSaturday, February 18, 12

What is needed? • Catalog of types of organisms • EMP • Niche information • Phenotypes and functions • Genetic diversity • Means for identification • Amateur participationSaturday, February 18, 12

What is needed? • Catalog of types of organisms • Biogeography (space & time); ranges • METADATA • Phenotypes and functions • Genetic diversity • Means for identification • Amateur participationSaturday, February 18, 12

Phylogenetic Diversity• Phylogenetic diversity poorly sampled• GEBA project at DOE- JGI correcting thisSaturday, February 18, 12

AMPHORA ALL Kembel et al. PLoS One 2011Saturday, February 18, 12

Wu and Eisen Genome Biology 2008 9:R151 doi:10.1186/gb-2008-9-10-r151Saturday, February 18, 12

New Markers 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 Dongying Wu et al. in prepSaturday, February 18, 12

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 ...Saturday, February 18, 12

Major phyla of bacteria & archaea No cultures Some culturesSaturday, February 18, 12

GEBA Uncultured Number of SAGs from Candidate Phyla 406 1 OD1 OP1 OP3 SAR Site A: Hydrothermal vent 4 1 - - Site B: Gold Mine 6 13 2 - Site C: Tropical gyres (Mesopelagic) - - - 2 Site D: Tropical gyres (Photic zone) 1 - - - Sample collections at 4 additional sites are underway. 46 Phil HugenholtzSaturday, February 18, 12

Functional Diversity? No cultures Some culturesSaturday, February 18, 12

Citizen Microbiology http://www.microbe.net/citizen-science-projects/ CITIZENMICROBIOLOGY.ORGSaturday, February 18, 12

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: OpennessSaturday, February 18, 12

What is needed? • Open publications • Open data • Open tools • Open discussion http://www.openmicrobiome.org/Saturday, February 18, 12

Plant/Animal Field StudiesSaturday, February 18, 12

Microbial Field StudiesSaturday, February 18, 12

MICROBESSaturday, February 18, 12

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 GilbertSaturday, February 18, 12

http://www.microbe.net	124
http://storify.com	27
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Towards a Field Guide to the Microbes for #AAASMtg

by Jonathan Eisen

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