Towards a Field Guide to the Microbes for #AAASMtg
1. Towards A Field Guide
to the Microbes
Jonathan A. Eisen
University of California, Davis
Twitter: @phylogenomics
AAAS Annual Meeting 2012
February 17, 2012
Saturday, February 18, 12
2. 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
Saturday, February 18, 12
15. II. More on Field Guides
Saturday, February 18, 12
16. 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
17. Diversity of Guild Guides
from Diane Schmidt at
http://www.library.illinois.edu/bix/fieldguides/index.html
Saturday, February 18, 12
23. 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
24. What is needed?
• Catalog of types of organisms
• Biogeography (space & time); ranges
• Niche information
• Phenotypes and functions
• Genetic diversity
• Means for identification
• Amateur participation
Saturday, February 18, 12
25. What is needed?
• Catalog of types of organisms
• Biogeography (space & time); ranges
• Niche information
• Phenotypes and functions
• Genetic diversity
• Means for identification
• Amateur participation
Saturday, February 18, 12
30. Mendeley Group
http://www.mendeley.com/groups/1359493/number-of-species-of-bacteria-and-archaea/
Saturday, February 18, 12
31. 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
32. Metagenomic Phylotpying
rRNA Phylotyping in
Sargasso Sea
Metagenomic
Metagenomic Data
Venter et al., Science
304: 66. 2004
Saturday, February 18, 12
33. Saturday, February 18, 12
Weighted % of Clones
0
0.1250
0.2500
0.3750
0.5000
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RecA
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Sargasso Phylotypes
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304: 66. 2004
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Metagenomic Phylotyping
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Venter et al., Science
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34. AMPHORA
Wu and Eisen
Genome Biology
2008 9:R151 doi:
10.1186/
gb-2008-9-10-
r151
Saturday, February 18, 12
35. Wu and Eisen Genome Biology 2008 9:R151 doi:10.1186/gb-2008-9-10-r151
Saturday, February 18, 12
36. 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.0018011
Saturday, February 18, 12
38. What is needed?
• Catalog of types of organisms
• Biogeography (space & time); ranges
• Niche information
• Phenotypes and functions
• Genetic diversity
• Means for identification
• Amateur participation
Saturday, February 18, 12
39. What is needed?
• Catalog of types of organisms
• EMP
• Niche information
• Phenotypes and functions
• Genetic diversity
• Means for identification
• Amateur participation
Saturday, February 18, 12
40. What is needed?
• Catalog of types of organisms
• Biogeography (space & time); ranges
• Niche information
• Phenotypes and functions
• Genetic diversity
• Means for identification
• Amateur participation
Saturday, February 18, 12
41. What is needed?
• Catalog of types of organisms
• Biogeography (space & time); ranges
• METADATA
• Phenotypes and functions
• Genetic diversity
• Means for identification
• Amateur participation
Saturday, February 18, 12
42. What is needed?
• Catalog of types of organisms
• Biogeography (space & time); ranges
• Niche information
• Phenotypes and functions
• Genetic diversity
• Means for identification
• Amateur participation
Saturday, February 18, 12
48. 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
49. Major phyla of bacteria & archaea
No cultures
Some cultures
Saturday, February 18, 12
50. 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 Hugenholtz
Saturday, February 18, 12
52. What is needed?
• Catalog of types of organisms
• Biogeography (space & time); ranges
• Niche information
• Phenotypes and functions
• Genetic diversity
• Means for identification
• Amateur participation
Saturday, February 18, 12
53. Citizen Microbiology
http://www.microbe.net/citizen-science-projects/
CITIZENMICROBIOLOGY.ORG
Saturday, February 18, 12
54. 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
Saturday, February 18, 12
55. What is needed?
• Open publications
• Open data
• Open tools
• Open discussion
http://www.openmicrobiome.org/
Saturday, February 18, 12
