The Earth Microbiome Project: Planetary Scale Systems Ecology
Sean M. Gibbons, Antonio González, Emmanuel Prestat, Jai Rideout, J. Gregory Caporaso, Rob Knight, Janet Jansson, and Jack A. Gilbert
Download EMP Data: http://www.microbio.me/emp EMP Website: http://www.earthmicrobiome.org/ Twitter: @gilbertjacka @gibbological
November 1, 2013
Argonne National Laboratory Institute for Genomic and Systems Biology
How many microbes on Earth?
~5x1030
~1x1023
How many stars in the observable universe?
What have we accomplished so far? Collaborators: 139 60,000 samples pledged 15,000 environmental samples being
processed 20,304 completed for 16S rRNA
analyses. Biomes Represented: 42 Total 16S rRNA Sequences:
1,713,425,117 Public data analysis led by EMP
working group Incredibly diverse set of metadata!
Metadata Standards
MIMARKS Environmental Packages
http://gensc.org/gc_wiki/index.php/MIMARKS
MIMARKS Environmental Packages
http://gensc.org/gc_wiki/index.php/MIMARKS
Genomic Biodiversity Working Interest Group- MIxS as RDF (https://code.google.com/p/mixs-as-rdf/)- MaterialSample proposal for the DwC Standard
Other Methodological and Analytical Standards
EMP 10K EMP has begun an analysis of the first ~10,000 samples
Recently finished the largest OTU picking run ever attempted…that we know of– 13,000 samples & 1.2 billion 16S reads– Run on Amazon EC2 M2.4xlarge spot instances using StarCluster– 11,000 processor consumed – 560 Gb – 1.3 Tb of RAM– 1.2 Tb of hard disc space
Results— ~10 million OTUs (97% identity)— 5,594,412 non-singleton OTUs
Questions/Goals— Novel Phyla/diversity— Phylogenetic overlap between and within biomes— Significant evidence for endemism, or allopatry— How much sampling is needed to sufficiently characterize an environment?— Who are the keystone species for different environments? Generalists vs. specialists?— Provide a framework for placing local datasets into a global context
Reuben et al., 2013, PLOS ONE
polar desert
tundrawarm desert
temperate
tropical
temperate forest
Get Involved! Membership defined by participation Send us your samples
– Why would the EMP help you address your hypotheses? What will your data contribute to the EMP?
– If you provide MIxS-compliant metadata, we sequence your samples! $$
Help analyze data through github
Acknowledgements Argonne National Laboratory: Jack Gilbert, Sarah Owens, Jarrad Marcelle, Daniel Smith,
Iraxte Zarraonaindia, Simon Lax, Kim Handley, Peter Larsen, Nicole Scott, and Chris Marshall
University of Chicago: Maureen Coleman, Jacob Waldbauer, Rick Stevens University of Colorado at Boulder: Rob Knight, Antonio Gonzáles Northern Arizona University: Greg Caporaso, Jai Rideout Berkeley National Laboratory: Janet Jansson, Emmanuel Prestat Graduate Program in Biophysical Sciences: Michele Wittels, Adam Hammond, Tobin Sosnick, Julie Feder
* Graduate Funding: EPA STAR Fellowship
Thanks for your attention! Questions?
Download EMP Data: http://www.microbio.me/emp EMP Website: http://www.earthmicrobiome.org/ Twitter: @gilbertjacka @gibbological
English Channel
Bog Lakes
Lake Mendota
Great Lakes
Maureen Coleman and Mark Anderson
Taxonomic Annotation Standards
16S
16S & 18S
Manually-curated full-length rRNA gene databases