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Interagency Report on the Federal Investment in Microbial Genomics - Appendices

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Navigation Banner Interagency Report on the Federal Investment In Microbial GenomicsForewardExecutive SummaryTable of ContentsIntroduction and ReportReferencesAppendix 1Appendix 2Appendix 3

APPENDIX 1 - FUNDING AGENCIES AND ORGANISMS OF RESEARCH

 

Funding
Agency

Organism

Phylogenetic Branch

Genome
Size

Project Description

Notes

URL1

DOD

Bacillus anthracis

Bacteria
Gram-positive

4.5 Mb

Genome sequencing

Pathogen; causes Anthrax; used in biological warfare

a

DOD

Plasmodium falciparum
Chr10,11 (isolate 3D7)

Eukaryote
Slime molds

2.1 Mb

Genome sequencing

Pathogen; malaria parasite

d

DOD

Pyrobaculum aerophilum

Archaea
Thermoproteus

2.2 Mb

Functional genomics

Hyperthermophile

a

DOE

Aquifex aeolicus

Bacteria
Aquifex

1.6 Mb

Genome sequenced, functional genomics

Chemolithoautotrophic thermophile

a

DOE

Archaeoglobus fulgidus

Archaea
Methanosarcina

2.2 Mb

Genome sequenced, functional genomics

Sulfur-metabolizing hyperthermophile

a

DOE

Carboxydothermus hydrogenoformans

Bacteria
Thermodesulfobacterium

1.8 Mb

Genome sequencing

Hydrogen production

 

DOE

Caulobacter crescentus

Bacteria
Purple bacteria

3.8 Mb

Genome sequencing

Used to study reg. of cell cycle events; bioremediation

a

DOE

Chlorobium tepidum

Bacteria
Green sulfur bacteria

2.1 Mb

Genome sequenced

Thermophilic photoautotroph, role in global carbon cycling

a

DOE

Clostridium acetobutylicum

Bacteria
Gram-positive

4.1 Mb

Genome sequenced

Industrial biotechnology & waste remediation

a

DOE

Dehalococcoides ethenogenes

Bacteria
Green nonsulfur bacteria

 

Genome sequencing

Anaerobic chemoautotroph useful for bioremediation

a

DOE

Deinococcus radiodurans

Bacteria
Deinococci

3.3 Mb

Genome sequenced

Chemoorganotroph, highly resistant to desiccation and gemma radiation

a

DOE

Desulfovibrio vulgaris

Bacteria
Purple bacteria

1.7 Mb

Genome sequencing

Sulfate-reducing bacteria; bioremediation

a

DOE

Geobacter sulfurreducens

Bacteria
Purple bacteria

1.0 Mb

Genome sequencing

Bioremediation

 

Appendix 1 continued

Funding
Agency

Organism

Phylogenetic Branch

Genome
Size

Project Description

Notes

URL1

DOE

Methanobacterium thermoautotrophicum

Archaea

Methanobacterium

1.8 Mb

Comparative & functional genomics

Methane-producing, moderate thermophile

a

DOE

Methanococcus jannaschii

Archaea
Methanococcus

1.7 Mb

Comparative & functional genomics

Autotrophic, methane-producing thermophile(also listed under NASA)

a

DOE

Mycoplasma genitalium

Bacteria
Gram-positive

0.6 Mb

Sequenced, functional genomics

Free-living organsim with smallest known genome

a

DOE

Nitrosomonas europaea

Bacteria
Purple bacteria

1.6 Mb

Genome sequencing

Carbon/nitrogen management

 

DOE

Nostoc spp.

Bacteria
Cyanobacteria

<10.0 Mb

Genome sequencing

Carbon management

 

DOE

Prochlorococcus marinus

Bacteria
Cyanobacteria

 

Genome sequencing

Carbon management

 

DOE

Pseudomonas putida

Bacteria
Purple bacteria

5.0 Mb

Genome sequencing

Opportunistic plant and animal pathogen; bioremediation

a

DOE

Pyrobaculum aerophilum

Archaea
Thermoproteus

2.2 Mb

Sequenced, functional genomics

Hyperthermophile; model for high temperature growth

a

DOE

Pyrococcus furiosus

Archaea
Thermococcus

2.1 Mb

Genome sequenced

Heterotrophic, sulfur-reducing thermophile

a

DOE

Rhodobacter capsulatus

Bacteria
Purple bacteria

3.7 Mb

Genome sequencing

Carbon and nitrogen fixation

k

DOE

Rhodopseudomonas palustris

Bacteria
Purple bacteria

<5.0 Mb

Genome sequencing

Hydrogen production

 

DOE

Shewanella putrefaciens Strain: MR-1

Bacteria
Purple bacteria

4.5 Mb

Genome sequencing

Model bacterial system for reductive dehalogenation reactions; bioremediation

a

Appendix 1 continued

Funding Agency

Organism

Phylogenetic Branch

Genome Size

Project Description

Notes

URL1

DOE

Thermotoga maritima

Bacteria

Thermotogales

1.9 Mb

Genome sequenced, functional genomics

Hyperthermophile; model for molecular mechanisms of protein thermostability

a

DOE

Thiobacillus ferrooxidans

Bacteria

Purple bacteria

2.9 Mb

Genome sequencing

Obligate chemolithoautotroph; carbon management, bioremediation

a

NASA

Methanococcus jannaschii

Archaea

Methanococcus

1.7 Mb

Comparative & functional genomics

Autotrophic, methane-producing thermophile (also listed under DOE)

a

NHGRI

Escherichia coli K-12

Bacteria Purple bacteria

4.6 Mb

Genome sequencing

Enteric bacteria

b

NHGRI

Saccharomyces cerevisiae

Eukaryote
Fungi

12.1 Mb

Genome sequencing, functional genomics

Yeast; model system for genetics & molecular bio.

c

NIAID

Chlamydia trachomatis
Strain: serovar D

Bacteria
Chlamydiae

1.0 Mb

Genome sequencing

Obligate intracellular pathogen, STD

d

NIAID

Enterococcus faecalis
Strain: V583

Bacteria
Gram-positive

3.2 Mb

Genome sequencing

Pathogen

d

NIAID

Escherichia coli
Strain: 0157:H7

Bacteria
Purple bacteria

4.6 Mb

Genome sequencing

Enteric bacteria; can cause severe foodborne disease

d

NIAID

Giardia lambia
Strain: WB 5 chrom.

Eukaryote
Diplomonads

 

Genome sequencing

Pathogen

d

NIAID

Leishmania major
Strain: Friedlin 36 chrom.

Eukaryote
Slime molds

0.3 Mb

Genome sequencing

Pathogen; causes cutaneous leishmaniasis

d

NIAID

Mycobacterium tuberculosis
Strain: CSU 93

Bacteria
Gram-positive

4.4 Mb

Genome sequencing

Pathogen; virulent clinical isolate

d

NIAID

Neisseria gonorrhoeae
Strain: FA1090

Bacteria
Purple bacteria

0.2 Mb

Genome sequencing

Pathogen; causes gonorrhea (STD)

d


Appendix 1 continued

Funding Agency

Organism

Phylogenetic Branch

Genome Size

Project Description

Notes

URL1

NIAID

Plasmodium falciparum Strain: 3D7 chr2,10,11

Eukaryote
Slime molds

3.1 Mb

Genome sequencing

Pathogen; malaria parasite

d

NIAID

Salmonella typhimurium

Bacteria
Purple bacteria

4.5 Mb

Genome sequencing

Pathogen; enteric bacteria

d

NIAID

Staphylococcus aureus Strain: 8325

Bacteria
Gram-positive

2.8 Mb

Genome sequencing

Pathogen; coagulase-positive staphylococci

d

NIAID

Staphylococcus aureus Strain: COL

Bacteria
Gram-positive

2.8 Mb

Genome sequencing

Pathogen; coagulase-positive staphylococci

d

NIAID

Streptococcus pneumoniae
Strain: 23F and 4

Bacteria
Gram-positive

2.1 Mb

Genome sequencing

Pathogen; common cause of bacterial pneumoniae

d

NIAID

Streptococcus pyogenes
Strain: M1 serotype class 1 rheumatogenic strain

Bacteria
Gram-positive

2.0 Mb

Genome sequencing

Pathogen; facultative anaerobe

d

NIAID

Treponema pallidum Strain: Nichols

Bacteria
Spirochetes

1.1 Mb

Genome sequencing

Pathogen; causes syphilis (STD)

d

NIAID

Trypanosoma brucei Strain: TREU 927/4

Eukaryote
Slime molds

 

Genome sequencing

Pathogen

d

NIAID

Ureaplasma urealyticum Strain: Serovar 3

Bacteria
Gram-positive

0.8 Mb

Genome sequencing

Pathogen

d

NIAID

Vibrio cholerae Strain: N16961, Serotype 01

Bacteria
Purple bacteria

2.5 Mb

Genome sequencing

Pathogen; causes cholera

d

NIDCR

Actinobacillus actinomycetemcomitans

Bacteria
Gram-negative

2.2 Mb

Genome sequencing

Oral pathogenic bacteria; causes periodontitis

g

NIDCR

Candida albicans

Eukaryote
Fungi

16.0 Mb

Genome sequencing

Opportunistic yeast; causes oral mucositis

h

NIDCR

Porphyromonas gingivalis

Bacteria
Gram-negative

2.2 Mb

Genome sequencing

Oral pathogenic bacteria; causes periodontitis

b, i

NIDCR

Streptococcus mutans

Bacteria
Gram-positive

2.2 Mb

Genome sequencing

Oral pathogenic bacteria; causes dental caries

b, j

Appendix 1 continued

Funding Agency

Organism

Phylogenetic Branch

Genome Size

Project Description

Notes

URL1

NIDCR

Treponema denticola

Bacteria
Spirochetes

3.0 Mb

Genome sequencing

Oral pathogenic bacteria; causes periodontitis

a

NIGMS

Escherichia coli

Bacteria
Purple bacteria

4.6 Mb

Functional genomics

Enteric bacteria

b

NIGMS

Methylobacterium extorquens

Bacteria
Purple bacteria

 

Genome sequencing

Methylotroph

b

NIGMS

Pyrobaculum aerophilum

Archaea Thermoproteus

2.2 Mb

Functional genomics

Hyperthermophile

a

NIGMS

Saccharomyces cerevisiae

Eukaryote
Fungi

12.1 Mb

Functional genomics

Yeast; model system for genetics & molecular bio.

c

NSF

Escherichia coli

Bacteria
Purple bacteria

4.6 Mb

Functional genomics

Genetic circuit analysis; comparative genomics, etc.

f

NSF

Halobacterium

Archaea
Halophiles

2.5 Mb

Genome sequencing, functional genomics

Halophilic

b

NSF

Neurospora crassa

Eukaryote
Fungi

43.0 Mb

EST sequencing & functional genomics

Developmental model for eukaryotic fungi

e

NSF

Synechococcus elongatus

Bacteria Cyanobacteria

2.7 MB

Genome sequencing, functional genomics

Model for photosynthetic and circadian rhythm studies

 

USDA

Pasteurella multocida

Bacteria
Purple bacteria

 

Genome sequencing

Pathogen; cause respiratory disease

b

1 Websites for additional information/links

  1. http://www.tigr.org/tdb/mdb/mdb.html
  2. http://geta.life.uiuc.edu/~nikos/genomes.html
  3. http://genome-www.stanford.edu/
  4. http://www.niaid.nih.gov/dmid/genome.htm
  5. http://biology.unm.edu/~ngp/home.html
  6. http://www-bioeng.ucsd.edu/research/research_groups/gcrg/index.html
  7. http://www.genome.ou.edu/act.html
  8. http://www-sequence.stanford.edu/group/candida/
  9. http://www.forsyth.org/pqqp/
  10. http://www.genome.ou.edu/smutans.html
  11. http://www.er.doe.gov/scripts/bes/ShowRecsx.asp

 


APPENDIX 2

 

Tree of Life

 

Tree of Life, from National Center for Genome Resources (http://www.ncgr.org/graphics/microbe/purple.gif)

 

APPENDIX 3

 

Examples of Genomics Websites:

http://www.nhgri.nih.gov/DIR/VIP/Glossary/ Glossary of genetic terms
http://www.ornl.gov/hgmis/publicat/glossary.html Glossary of genetic terms
http://www.ornl.gov/hgmis/resource/education.html

Human genome education resource (links to curriculum, contacts, etc).

http://www.kumc.edu/gec/ Humane genetics education center
http://www.nhgri.nih.gov/Data/ Genome resources on the web
http://www.nhgri.nih.gov/DIR/VIP/ Science and education outreach page
http://www.tigr.org/ List of finished and ongoing genome projects with funding agency identified.
http://geta.life.uiuc.edu/~nikos/genomes.html List of genome projects, links to taxonomy and functional genomics databases.
http://www.proteome.com/ Proteomic database - this is an example of an industry/grant funded genomics-level database. It was originally developed for S. cerevisiae.

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CONTENTS | INTRODUCTION | DOD | DOE | NASA | NIH | NIST | NSF | USDA | GAPS\OPPORTUNITIES | REFERENCES | APPENDIX 1 | APPENDIX 2 | APPENDIX 3


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