1. Cyber Metagenomics; Challenge to See The Unseen Majority in The Ocean
Kayo Arima
California Institute for Telecommunications and Information Technology (Calit2)-University of California, San Diego Division

2. Science Falkowski and Vargas 304 (5667): 58
Looking Back Nearly 4 Billion Years In the Evolution of Microbe Genomics
Eukaryote has the nuclei .
Prokaryotes has genes but
no nuclear membrane.
Science Falkowski and Vargas 304 (5667): 58

3. Much of Genome Work Has Occurred in Animals
Evolution is the Principle of Biological Systems: Most of Evolutionary Time Was in the Microbial World
You Are Here
Much of Genome Work Has Occurred in Animals
Source: Carl Woese, et al

4. Two completely different approach to get microbial genomic information
Microbial whole genomics
Metagenomics
Environmental sample
Culture (grow) in lab
Isolate the colony
Culture the isolated colony
DNA extraction
Enz. digestion
Shotgun sequencing
Gene assembly
Environmental sample
DNA extraction
Enz. digestion
Shotgun sequencing
Scaffold assembly
                
Source: Karin Remington
J. Craig Venter Institute

5. Down Side of Metagenomics
Often fragmentary
Often highly divergent
Rarely any known activity
No chromosomal placement
No organism of origin
Ab initio ORF predictions
Huge data

6. GenBank Protein Data Bank
Genomic Data Is Growing Rapidly, But Metagenomics Will Vastly Increase The Scale…
100 Billion Bases!
35,000 Structures
GenBank
Protein Data Bank
Total Data < 1TB

7. First Genome 1995 6 Genomes/ Year 2000
Full Genome Sequencing is Exploding: Most Sequenced Genomes are Bacterial
First Genome Genomes/ Year 2000
Ongoing Genomes
Completed Genomes 90
Metagenomes
Total 422
Total 1665

8. Marine Metagenomics
Microbes account for more than 90% of ocean biomass, mediate all biochemical cycles in the oceans and are responsible for 98% of primary production in the sea.
Metagenomics is a breakthrough sequencing approach to examine the open-space microbial species without the need for isolation and lab cultivation of individual species.

9. PI Larry Smarr
Paul Gilna Ex. Dir.
PI Larry Smarr

10. Marine Genome Sequencing Project Measuring the Genetic Diversity of Ocean Microbes
Sorcerer II Data from this area has already reach to 10% of GenBank.
The Entire Data Will Double Number of Proteins in Embank!

11. Sample Metadata from GOS
Site Metadata
Location (lat/long, water depth)
Site characterization (finite list of types plus “other”)
Site description (free text)
Country
Sampling Metadata
Sample collection date/time
Sampling depth
Conditions at time of sampling (e.g., stormy, surface temperature)
Sample physical/chemical measurements (T (oC), S (ppt), chl a (mg m-3), etc)
“author”
Experimental Parameters
Filter size
Insert size

12. Flat File
Server
Farm
W E B PORTAL
Traditional
User
Response
Request
Dedicated
Compute Farm
(1000 CPUs)
TeraGrid: Cyberinfrastructure Backplane
(scheduled activities, e.g. all by all comparison)
(10000s of CPUs)
Data-
Base
10 GigE
Fabric
Calit2’s Direct Access Core Architecture Will Create Next Generation Metagenomics Server
Source: Phil Papadopoulos, SDSC, Calit2
+ Web Services
Sargasso Sea Data
Sorcerer II Expedition (GOS)
JGI Community Sequencing Project
Moore Marine Microbial Project
NASA Goddard Satellite Data
Community Microbial Metagenomics Data
Web
(other service)
Local
Cluster
Environment
Direct
Access
Lambda
Cnxns

13. Who is there? Marine Metagenomics Metabolic pathway discovery
Drug discovery
Microbial genetic survey
Environmental survey
Symbiosis
Who is there?
Evolution study
Endosymbiosis
Organism discovery
Microbial genomic survey
Bioenergy discovery
Biogeochemistry mapping
Marine conservation