Interagency Report on the Federal Investment in Microbial Genomics

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

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.