1% of microbes are culturable

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Ecogenomics A New Frontier

• lt 1 of microbes are culturable
• Many unculturables live in interdependent
  consortia of considerable diversity
• Ecogenomics applying the tools of genomics,
  proteomics, etc to ecology
• Can we recover genome-scale sequences and reveal
  metabolic capabilities?
• What is the structure of natural microbial
  populations? How do they interact? Are they
  interdependent?
• Can we harness their metabolic capabilities?

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Ecogenomics Studying an environment with
minimal microbial complexity
Iron Mountain - microbially mediated toxic metal
discharge Superfund Site, pH lt 1

• Biofilm with a few uncultured organisms
• Identification, through genome assembly, of
  the organisms present and responsible
• Understanding of microbial interactions,
  roles and molecular mechanisms could lead to
  biochemical solutions

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Microbial Solutions from
the Sargasso Sea?

• Institute for Biological Energy Alternatives
• Collection of 200 L samples with shotgun
  sequencing
• Preliminary analysis suggests presence of 1,600
  species

• Identification of gt1.3 million new genes
• Discovery of 800 distinct rhodopsin homologs
  (light-sensitive photoreceptors)
• Understanding the genetic and biochemical
  diversity in our oceans may lead to new methods
  for carbon sequestration or alternative energy
  production.

4
Environmental Sample
Purify High Molecular Weight DNA
Fosmid Library Construction
Shotgun Library Construction



Fosmid Insert End Sequencing

DNA Sequencing
Assembly Annotation
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Environmental Sample
Purify High Molecular Weight DNA
When possible culture isolates
Fosmid Library Construction

Fosmid Insert End Sequencing
DNA Sequencing
Assembly Annotation
?

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