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Causes Lyme disease

<P> <I><B>Borrelia burgdorferi</I> strain B31</B>. This is the type strain (ATCC 35210) for this organism and was derived by limited dilutional cloning from the original Lyme-disease tick isolate derived by A. Barbour.

Borreliella burgdorferi B31

PRJNA3

2001-01-09T00:00:00Z

Causes periodontal disease, gum inflamation

<P><I><B>Treponema denticola</I> ATCC 35405</B>. <I>Treponema denticola</I> ATCC 35405 was isolated from a human periodontal pocket and is the type strain of this organism.

Treponema denticola ATCC 35405

PRJNA4

2004-02-03T00:00:00Z

Causative agent of syphilis

<P><I><B>Treponema pallidum</I> subsp. <I>pallidum</I></B>. This organism is the causative agent of endemic and venereal syphilis. This sexual transmitted disease was first discovered in Europe at the end of the fifteenth century, however, the causative agent was not identified until 1905. At one time syphilis was the third most commonly reported communicable disease in the USA. Syphilis is characterized by multiple clinical stages and long periods of latent, asymptomatic infection. Although effective therapies have been available since the introduction of penicillin, syphilis remains a global health problem. <P><I><B>Treponema pallidum</I> subsp. <I>pallidum</I> strain Nichols</B>. This strain was originally isolated in 1912 from a neurosyphilitic patient and is virulent.

Treponema pallidum subsp. pallidum str. Nichols

PRJNA5

2001-01-09T00:00:00Z

Causes infertility, infectious abortions, septicemia, meningitis

<P> <B><I>Campylobacter fetus</I> subsp. <I>venerealis</I> str. Azul-94</B>. Field isolate obtained from an aborted Bos taurus (cow) fetus (Year: 1994, Place: Tandil, Argentina).

Campylobacter fetus subsp. venerealis str. Azul-94

PRJNA7

2009-04-22T00:00:00Z

Leading cause of food poisoning (altered virulence strain)

<P> <B><I> Campylobacter jejuni</I> strain NCTC11168</B>. This strain (originally 5636/77) was isolated from a diarrheic patient in 1977 and minimally passaged. This strain displays aberrant virulence phenotypes in animal models and tissue culture. Contains many homopolymeric tracts in the genome which result in hypervariable sequences in many genes having to do with cell surface structures. These sequences result in hypervarible antigenic diversity and immune evasion. Overall, the genome contains very few repetitive DNA sequences and very few coding regions arranged in operons. Pathogenicity factors include cytolethal-distending toxin, hemolysin-like toxins, and a type II secretion system.

Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

PRJNA8

2003-05-06T00:00:00Z

Aquatic bacterium that cause tularemia

<P> <B><I>Francisella tularensis</I> subsp. <I>tularensis</I> strain Schu S4</B>. This subspecies is virulent in humans, and the strain is a clinical isolate that is also virulent in an animal model. Originally isolated from a human case of tularemia in 1951. Genome analysis indicates the presence of a large number of pseudogenes, many that disrupt important metabolic pathways, which is the reason for the exacting nutritional requirements of this organism. There is a duplicated pathogenicity island that has also been detected in strain LVS and mutations in the <i>iglA</i>, <i>iglC</i>, or <i>pdpD</i> genes affect the ability of the pathogen to survive in macrophages. The genome also contains genes for type IV pili production and capsular polysaccharide genes similar to those of Bacillus anthracis as well as numerous ABC transporters. There are a large number of insertion sequences including a mariner element, which is a transposon typically found in eukaryotes and is the first instance of this element to be found in a microbe, which may have acquired it during transit through one of the insect vectors.

Francisella tularensis subsp. tularensis SCHU S4

PRJNA9

2004-12-14T00:00:00Z

Microorganism of putrefaction

<P> <B><I>Pseudomonas fluorescens</I> strain Pf0-1</B>. This strain was isolated from agricultural loam (sand, clay, and organic matter) soil in 1988 by Compeau <I>et al</I>. and is well adapted to soil environments.

Pseudomonas fluorescens Pf0-1

PRJNA12

2005-10-07T00:00:00Z

Soil-born pathogen that naturally infects plant roots

<p> <B><I>Ralstonia solanacearum</I> strain GMI1000</B>. This strain is a race 1 strain isolated from the tomato plant and is also pathogenic on <I>Arabidopsis thaliana</I>. It specifically invades the plant xylem. <P> Pathogenicity factors include an extracellular polysaccharide that protects the bacterium and a type III secretion system (the <I>hrp</I> system) that is encoded on the megaplasmid and delivers effector molecules such as avirulence (Avr) proteins into the host cell. There is a type II secretion system for export of degradative enzymes such as plant cell wall hydrolases. This organism expresses a large number of outer membrane proteins including several that are related to hemagglutinins, as well as numerous fimbriae, including a type IV pilus for attachment and twitching motility. The two chromosomes contains many copies of insertion elements.

Ralstonia pseudosolanacearum GMI1000

PRJNA13

2003-05-06T00:00:00Z

Causes black rot and citrus canker

<p> <B><I>Xanthomonas campestris</I> pv. <i>campestris</i> strain 8004</B>. This strain is a derivative of strain NCPBB No. 1145. The original was isolated from an inflected cauliflower in Sussex, United Kingdom, in 1958. Strain 8004 is a spontaneous rifampicin resistant strain and has been used extensively in many studies.

Xanthomonas campestris pv. campestris str. 8004

PRJNA15

2005-05-25T00:00:00Z

Nitrogen-fixing bacterium

<P><B><I>Azotobacter vinelandii</B></I>. This organism will provide information on the proteins involved in nitrogen fixation and the production of PHB and alginate.

Azotobacter vinelandii DJ strain:DJ

PRJNA16

2009-04-14T00:00:00Z

Nitrogen-fixing plant symbiont

<P> <B><I>Bradyrhizobium japonicum</I> strain USDA110</B>. This strain was isolated from Glycine hispida in 1959 in Florida, USA, and has been widely studied because of its superior symbiotic nitrogen fixation with soybeans as compared to other strains. This strain contains a 681 Kb symbiosis island that contains genes for nitrogen fixation and root nodule formation. The chromosome also contains genes resembling those of type III and IV secretion systems. <P> The original strain designation of USDA110 was 3I1b110, which was gradually changed to USDA110 in the early 1960's with the development of serology and the recognition that 17 different serogroups could be distinguished. USDA110 is the serotype strain for the "110" serogroup. The type strain of the species is Bradyrhizobium japonicum USDA 6 which was isolated from soybean in Japan. USDA acquired this culture from the University of Tokyo in 1929. This culture has a different serogroup affinity to USDA 110 and is in fact the serotype strain of the 6 serogroup.

Bradyrhizobium diazoefficiens USDA 110

PRJNA17

2004-05-11T00:00:00Z

Symbiotic nitrogen-fixing bacteria

<P> <B><I>Mesorhizobium loti</I> strain MAFF303099</B>. This strain contains 2 plasmids as well as a symbiotic island that is 610 Kb on the chromosome that is significantly divergent as compared to the symbiotic island of <I>Mesorhizobium loti</I> strain ICMP3153 but does contain root nodule formation and nitrogen-fixation genes. The symbiosis island contains genes similar to those for type III and IV secretion systems. Both plasmids pMLa and pMLb contain genes similar to type IV secretion genes.

Mesorhizobium japonicum MAFF 303099

PRJNA18

2004-05-11T00:00:00Z

Nitrogen-fixing bacterium

<P> <B><I>Sinorhizobium meliloti</I> strain 1021</B>. Streptomycin resistant derivative of strain 2011. This strain carries 2 megaplasmids, pSymA and pSymB. Nitrogen fixation functions and nodulation genes are found on pSymA. The second plasmid encodes a number of transport systems, including many ABC-type transporters. This organism does not have a type III secretion system like the other Rhizobia but does have a type IV secretion system.

Sinorhizobium meliloti 1021

PRJNA19

2003-05-06T00:00:00Z

Methanol-utilizing bacterium

<P> <B><I>Methylobacterium extorquens</I> strain AM1</B>. This strain can grow on methylamine or methanol, but not methane. It is an extensively studied laboratory strain.

Methylorubrum extorquens AM1

PRJNA20

2009-06-17T00:00:00Z

Uses methane as sole carbon and energy source

<P><B><I>Methylococcus capsulatus</I> str. Bath</B>. This organism will provide information on the proteins involved in methane oxidation.

Methylococcus capsulatus str. Bath

PRJNA21

2004-10-04T00:00:00Z

Aquatic bacterium that causes Legionnaire's disease

<p> <B><I>Legionella pneumophila</I> subsp.<I> pneumophila</I> str. Philadelphia 1</B>. This strain is the isolate from the initial event of Legionellosis in Philadelphia and is the type strain for this species.

Legionella pneumophila subsp. pneumophila str. Philadelphia 1

PRJNA22

2004-09-24T00:00:00Z

Causes gonorrhea

<P> <B><I>Neisseria gonorrhoeae</I> strain FA 1090</B>. A serum-resistant streptomycin-resistant proline-requiring strain isolated from a patient with disseminated gonococcal infections.

Neisseria gonorrhoeae FA 1090

PRJNA23

2005-02-14T00:00:00Z

Causes respiratory diseases

<P> <B><I>Bordetella bronchiseptica</I> strain RB50</B>. This strain was isolated from a rabbit. The genome contains a type IV pilus biosynthetic operon that produces pili for attachment. The chromosome also contains the gene for pertussis toxin but it is not expressed.

Bordetella bronchiseptica RB50

PRJNA24

2003-08-12T00:00:00Z

Causes bronchitis and other respiratory deseases

<P> <B><I>Bordetella parapertussis</I> strain 12822 </B>. This strain was isolated from an infected infant in Germany in 1993. The genome contains the gene for pertussis toxin but does not express it.

Bordetella parapertussis 12822

PRJNA25

2003-08-12T00:00:00Z

Causes bronchitis and other respiratory deseases

<P> <B><I>Bordetella pertussis</I> Tohama I</B>. This strain was originally isolated from a patient with whooping cough and has been studied extensively for over 40 years. The chromosome contains a type IV secretion system for export of the pertussis toxin, a typical AB type toxin. The B subunits are involved in attachment to host cells, and the A subunit, the ADP-ribosylating factor, interferes with cell signalling pathways by increasing intracellular cAMP concentrations. The result is an inability of phagocytes to kill foreign invaders such as the bacterium.

Bordetella pertussis Tohama I

PRJNA26

2003-08-12T00:00:00Z

Causes bordetellosis

<P> <B><I>Bordetella avium</I> strain 197N</B>. This strain is a spontaneous nalidixic acid-resistant derivative of virulent strain 197.

Bordetella avium 197N

PRJNA27

2006-09-29T00:00:00Z

Opportunistic pathogen that causes soft rot disease in plants

<P> <B><I> Dickeya dadantii</I> strain 3937</B>. Formerly <I>Erwinia chrysanthemi</I>, this strain (3937) is wild-type and was isolated from <I>Saintpaulia</I> plants. It is a well characterized strain and has been used extensively. It produces important exoenzymes, including 5 types of pectinases, pectin methylesterases and an acetylesterase for degradation of modified plant cell wall components. <P>Recent taxonomic revisions have altered the name of this organism over the course of the genome project; This organism is now named <I>Dickeya dadantii</I>, but was previously named <I>Erwinia chrysanthemi</I> and <I>Pectobacterium chrysanthemi</I>. <I>Dickeya dadantii</I> is an important model system for studying the molecular basis and regulation of soft-rot pathogenesis. Soft-rot associated enterobacteria cause devastating disease on a wide range of plant host species including agriculturally important crops and ornamentals. Most of the genome sequencing took place at The Institute for Genomic Reasearch (TIGR) with final gap closure and finishing at the University of Wisconsin. An international network of collaborators worked with GEL personnel to annotate and analyze this genome sequence.

Dickeya dadantii 3937

PRJNA30

2010-09-10T00:00:00Z

Opportunistic pathogen that causes multiple hospital-acquired infections

<B><I> Klebsiella pneumoniae </I> subsp.<I> pneumoniae</I> strain MGH 78578</B>. This strain was isolated from a patient in 1994.

Klebsiella pneumoniae subsp. pneumoniae MGH 78578

PRJNA31

2007-07-05T00:00:00Z

Major cause of food poisoning in US

<P> <B><I>Salmonella enterica</I> subsp. <I>enterica</I> serovar Enteritidis strain LK5</B>. This serovar, also known as <I>Salmonella enteritidis</I>, is often associated with salmonellosis and is the major cause of food poisoning in the United States (gastroenteritis) due to the advent of mass chicken egg production. It is the only human pathogen in the <I>Salmonella</I> group that routinely contaminates chicken eggs, although it does not cause discernible disease in the chicken. This strain was isolated from a chicken.

Salmonella enterica subsp. enterica serovar Enteritidis str. LK5

PRJNA32

Fowl-adapted Salmonella

<P> <B><I>Salmonella enterica</I> subsp. <I>enterica</I> serovar Pullorum</B>. This serovar is fowl-adapted and causes dysentery.

Salmonella enterica subsp. enterica serovar Pullorum

PRJNA33

Extremely virulent organism that causes plague

<P> <B><I>Yersinia pestis</I> strain CO92</B>. This strain is a recent Orientalis subtype isolated in the USA from a patient who died of pneumonic plague after acquiring the disease from an infected cat. This strain is 50 Kbp larger than the <I>Yersinia pestis</I> KIM10+ genome due to numerous insertions.

Yersinia pestis CO92

PRJNA34

2003-05-06T00:00:00Z

Aquatic organism that causes Cholera

<P> <B><I>Vibrio cholerae</I> O1 biovar ElTor str. N16961</B>. This is an epidemic serogroup of <I>Vibrio cholerae</I> isolated in 1971 in Bangladesh and is distinguished from the classical biotype due to hemolysin production. It contains 2 chromosomes. The first, and larger chromosome, contains many essential cell functions, as well as virulence genes contained within pathogenicity islands (PAIs). One major pathogenicity determinant is encoded within a PAI that is contained inside an integrated phage (CTXphi) on chromosome 1 that codes for the cholera toxin, an adenylate cyclase. Once the toxin is injected into host cells, it results in secretion of chlorine ions, which leads to increased water secretion, dehydration, and eventually, death. Up to 20 litres of water a day may be lost. The second chromosome also has important cell functions, but has a preponderance of genes associated with energy and transport functions, including signal transduction systems, and in addition, DNA repair enzymes. Chromosome 2 also has the integron island, a large variable region of the chromosome that functions as a gene capture system, some of which are associated with antibiotic resistance. There are 105 genes that have copies on both chromosomes.

Vibrio cholerae O1 biovar El Tor str. N16961

PRJNA36

2001-01-09T00:00:00Z

Obligate pathogen that causes sexually-transmitted chancroid and enhances HIV transmission

<P> <B><I> Haemophilus ducreyi </I>35000HP </B>. This strain is a human passage derivative of <I>Haemophilus ducreyi</I> strain 35000 that is serum-resistant.

[Haemophilus] ducreyi 35000HP

PRJNA38

2003-07-23T00:00:00Z

Opportunistic pathogen that causes a range of infections in humans and animals

<P><B><I>Pasteurella multocida</I> subsp. <I>multocida</I> str. Pm70</B>. <I>Pasteurella multocida</I> subsp. <I>multocida</I> str. Pm70 was isolated in 1995 from a case of fowl cholera in chickens. This strain is a serotype 3 capsular type A strain and will provide information on the production and regulation of proteins involved in virulence and disease.

Pasteurella multocida subsp. multocida str. Pm70

PRJNA39

2001-03-21T00:00:00Z

Causes bovine anaplasmosis

<P> <B><I> Anaplasma marginale</i> strain St. Maries</b>. This strain was recovered from an acutely infected cow from Northern Idaho and bears an msp1a genotype of JBB. This strain is transmitted by ticks and is known to be virulent.

Anaplasma marginale str. St. Maries

PRJNA40

2004-12-06T00:00:00Z

Nine Mile phase I isolate that causes Q fever

<P> <B><I> Coxiella burnetii </I> strain RSA 493</B>. This is a Nine Mile phase I isolate which contains a small plasmid QpH1.

Coxiella burnetii RSA 493

PRJNA41

2003-04-04T00:00:00Z

Obligate intracellular pathogen that causes Rocky Mountain Spotted Fever

<P> <B><I> Rickettsia conorii</I> strain Malish 7</B>. This strain was isolated from a human in South Africa.

Rickettsia conorii str. Malish 7

PRJNA42

2002-11-25T00:00:00Z

Causes louse-borne typhus and Mediterranean spotted fever (avirulent strain)

<P> <B><I> Rickettsia prowazekii</I> strain Madrid E</B>. This strain is an egg-passaged attentuated avirulent strain that has been used as a live vaccine and was originally isolated from a typhus patient in Madrid.

Rickettsia prowazekii str. Madrid E

PRJNA43

2003-05-06T00:00:00Z

Causes bacillary angiomatosis

<P> <B><I>Bartonella quintana</I> str. Toulouse</B>. <I>Bartonella quintana</I> str. Toulouse was isolated from human blood in Toulouse, France in 1993. There is evidence of extensive genome reduction in comparison to other <I>Bartonella</I> species which may be associated with the limited host range of <I>Bartonella quintana</I>.

Bartonella quintana str. Toulouse

PRJNA44

2004-06-25T00:00:00Z

Serovar D strain that causes pharyngitis, bronchitis and pneumonitis

<P> <I><B>Chlamydia trachomatis</I> strain D/UW-3/CX</B>. This is a trachoma biovar, serovar D strain.

Chlamydia trachomatis D/UW-3/CX

PRJNA45

2001-01-09T00:00:00Z

Opportunistic pathogen of mammalian intestinal tract

<P> <B><I>Bacteroides fragilis</I> strain ATCC 25285</B>. This organism can become an opportunistic pathogen, infecting anywhere in the body and causing abcess formation. Enterotoxigenic <I>Bacterioides fragilis</I> (ETBF) is associated with diarrheal diseases. This strain is the type strain.

Bacteroides fragilis NCTC 9343 strain:ATCC 25285

PRJNA46

2005-03-03T00:00:00Z

Rumen cellulolytic bacteria

<P><B><I>Fibrobacter succinogenes</I> subsp. <I>succinogenes</I> strain S85</B>. The production of cellulolytic enzymes by <I>Fibrobacter succinogenes</I> subsp. <I>succinogenes</I> strain S85 has been extensively studied. Strain S85 is the type strain for this organism and the genome sequence will provide information on the production and regulation of these enzymes.

Fibrobacter succinogenes subsp. succinogenes S85

PRJNA47

2010-08-06T00:00:00Z

Bacterium associated with periodontal disease

<B><I>Porphyromonas gingivalis</I> strain W83</B>. This strain (also known as HG66) is virulent in a mouse model and has been extensively studied. It was originally isolated by H. Werner in the 1950s in Bonn, Germany, from an unknown human infection. <P>

Porphyromonas gingivalis W83

PRJNA48

2003-09-02T00:00:00Z

Aerotolerant organism that causes ovine footrot

<I><B>Dichelobacter nodosus</i> strain VCS1703A</b>. This strain is a virulent type G strain which is naturally transformable and has been used in virulence studies.

Dichelobacter nodosus VCS1703A

PRJNA50

2007-05-04T00:00:00Z

Bacterium capable of metal corrosion

<P> <B><I> Desulfovibrio vulgaris</I> subsp. <I>vulgaris</I> strain Hildenborough</B>. This strain was isolated from clay soil near Hildenborough, UK in 1946. A plasmid containing genes that encode <I>nif</I> functions (nitrogen fixation) as well as a type III secretion system (TTSS) is found in this organism The function of the TTSS genes is unknown.

Nitratidesulfovibrio vulgaris str. Hildenborough

PRJNA51

2004-04-21T00:00:00Z

Nitrifying bacterium

<P><I><B>Nitrosomonas europaea</I> ATCC 19718</B>. The chromosome of <I>Nitrosomonas europaea</I> ATCC 19718 contains numerous gene and DNA duplications, including those for the oxidation of ammonia, which may be due to the numerous insertion sequences also present.

Nitrosomonas europaea ATCC 19718

PRJNA52

2003-05-06T00:00:00Z

Acidophile used for bioremediation and recovery of important metals

<P><B><I>Acidithiobacillus ferrooxidans</I> ATCC 23270</B>. This organism was isolated from bituminous coal mine effluent. The genome sequence of this organism will provide information on the production and regulation of proteins involved in iron-oxidation and will be used for comparative analysis with other iron-oxidizing bacteria.

Acidithiobacillus ferrooxidans ATCC 23270

PRJNA53

2008-12-19T00:00:00Z

Abundant soil organism that degrades cellulose

<P><B><I>Cytophaga hutchinsonii</I> ATCC 33406</B>. The genome sequence of this strain will provide information on the production and regulation of proteins involved in the degradation of chitin, cellulose and other compounds.

Cytophaga hutchinsonii ATCC 33406

PRJNA54

2006-07-11T00:00:00Z

A bacterium with alternative energy-converting pathways.

<p> <b><i>Rhodobacter capsulatus</i> strain SB1003</b>. This strain is a derivative strain isolated in the laboratory of Barry Marrs from the classical progenitor strain B10. It is rifampicin-resistant, produces GTA, and is capable of growing under high illumination (resistant to photooxidative killing). <p>

Rhodobacter capsulatus SB 1003

PRJNA55

2010-04-09T00:00:00Z

Metabolically diverse phototrophic bacterium

<P> <B><I>Rhodobacter sphaeroides</i> strain 2.4.1</b>. This is the type strain for this organism.

Cereibacter sphaeroides 2.4.1

PRJNA56

2005-10-07T00:00:00Z

Metabolically diverse organism important in carbon cycle and bioremediation

<P> <B><I>Rhodopseudomonas palustris</I> strain CGA009</B>. This organism contains genes for bacteriochlorophyll and carotenoid synthesis as well as genes for the light reaction center that allow photophosphorylation in addition to carbon (RubisCO) and nitrogen fixation (nitrogenase) genes. It also has genes for the oxidation of inorganic compounds such as thiosulfate and hydrogen and nitrogenases for nitrogen fixation. This bacterium can degrade aromatic compounds and the genome encodes a large repertoire of degradative enzymes. There are a type II, type III, and two type IV secretion systems on the chromosome, and the organism also contains a small cryptic plasmid.

Rhodopseudomonas palustris CGA009

PRJNA57

2003-12-11T00:00:00Z

Bacterium that can grow using anoxygenic photosynthesis

<P><B><I>Rhodospirillum rubrum</I> ATCC 11170</B>. This bacterium can grow using carbon monoxide as the sole carbon and energy source and the cells contain a well characterized nitrogenase system that is post-translationally modified by ADP-ribosylation.

Rhodospirillum rubrum ATCC 11170

PRJNA58

2005-12-12T00:00:00Z

Thermophilic phototroph

<P><B><I>Chloroflexus aurantiacus</I> J-10-fl</B>. <I>Chloroflexus aurantiacus</I> J-10-fl (DSM 635) was isolated from the Hakone hot spring area in Japan and will be used for comparative analysis.

Chloroflexus aurantiacus J-10-fl

PRJNA59

2007-12-20T00:00:00Z

Model cyanobacterium for analysis of photosynthetic organisms

<P><B><I>Synechocystis</I> sp. PCC 6803</B>. This cyanobacterium was isolated from a freshwater lake in 1968 and is easily transformed by exogenous DNA. The photosynthetic apparatus is very similar to the one found in plants. This organism also exhibits phototactic movement.

Synechocystis sp. PCC 6803

PRJNA60

2004-05-11T00:00:00Z

Cellulolytic bacterium that inhabits rumen

<P><B><I>Ruminococcus albus</I> strain 8</B>. <I>Ruminococcus albus</I> strain 8 was isolated from an alfalfa hay-fed cow. Cellulose degradation has been extensively studied in this organism and the genome sequence will provide information on the production and regulation of proteins involved in this process.

Ruminococcus albus 8 strain:8

PRJNA62

2010-03-25T00:00:00Z

Associated with mastitis in cattle

<P> <I><B>Staphylococcus aureus</I> strain RF122</B>. This strain is a common strain associated with mastitis in cattle. This organism is responsible for several hundred million dollars worth of annual economic loss to animal production each year

Staphylococcus aureus RF122

PRJNA63

2005-11-24T00:00:00Z

Pathogenic clinical isolate that causes toxic-shock syndrome and staphylococcal scarlet fever

<P> <I><B>Staphylococcus epidermidis</I> strain RP62A</B>. This strain is a strongly adherent, slime-producing, pathogenic strain isolated from a patient with intravascular catheter-associated sepsis.

Staphylococcus epidermidis RP62A

PRJNA64

2005-01-13T00:00:00Z

Extremely radiation-resistant soil bacterium

<P> <B><I> Deinococcus radiodurans</I> strain R1</B>. This strain was reported as the R1 type strain, ATCC 13939. However, it was later stated that this strain is really the USUHS strain at the Uniformed Services University in Bethesda, Maryland, and has acquired nucleotide substitutions as compared to the R1 strain. It is known as ATCC BAA-816.

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 strain:R1

PRJNA65

2000-12-11T00:00:00Z

Causes caries and periodontal diseases

<P> <I><B>Streptococcus gordonii</I> strain Challis</B>. This strain is used extensively in the laboratory because of its well characterized transformation system.

Streptococcus gordonii str. Challis substr. CH1

PRJNA66

2007-09-11T00:00:00Z

Opportunistic pathogen that transfers vancomycin resistance to other bacteria

<P> <B><I>Enterococcus faecalis</I> strain V583</B>. This strain is one of the first vancomycin-resistant strains isolated. This isolate came from a blood culture derived from a chronically-infected patient in 1987 from Barnes Hospital in St. Louis, Missouri. This strain was found to lack the cytolysin gene and a surface adhesin, Esp, that contributes to urinary tract infections. Mobile genetic elements make up one quarter of the genome.

Enterococcus faecalis V583

PRJNA70

2003-03-28T00:00:00Z

Opportunistic pathogen that transfers vancomycin resistance to other bacteria

<P> <B><I>Enterococcus faecium</I> DO</B>. <I>Enterococcus faecium</I> DO is an opportunistic pathogen that transfers vancomycin resistance to other bacteria.

Enterococcus faecium DO strain:DO

PRJNA71

2002-07-10T00:00:00Z

Used extensively in soft cheese production

<P> <B><I>Lactococcus lactis</I> subsp. <I>lactis</I></B>. This subspecies is used to make soft cheeses. <P> <B><I>Lactococcus lactis</I>subsp.<I> lactis</I> Il1403</B>. This strain is used widely in laboratory research and is a plasmid-free derivative of strain IL594 isolated from a cheese starter culture. The genome shows many insertion sequences and prophages, and surprisingly, a large number of genes involved in respiration, suggesting that this organism may aerobically respire.

Lactococcus lactis subsp. lactis Il1403

PRJNA72

2001-03-21T00:00:00Z

Soil organism that causes opportunistic infections such as food poisoning

<P> <B><I>Bacillus cereus</I> strain ATCC 10987</B>. This strain was isolated in Canada during a study of cheese spoilage. It contains a plasmid, pBc10987, that is similar to Bacillus anthracis toxin plasmid pXO1, but lacks the anthrax toxin genes.

Bacillus cereus ATCC 10987

PRJNA74

2004-02-23T00:00:00Z

Thermophilic organism that produces thermostable spores and stable enzymes that are used in industry

<P> <B><I>Geobacillus stearothermophilus</I> strain 10</B>. This strain was isolated from a hot spring in Yellowstone National Park and has been used in comparative analyses of thermophilic (high temperature) and mesophilic (medium temperature) <I>Bacillus</I> spp..

Geobacillus stearothermophilus 10 strain:10

PRJNA75

Model organism for prokaryotic cell differentiation and development

<P> <B><I>Bacillus subtilis</I> subsp.<I> subtilis</I> str. 168</B>. This strain was derived in 1947 from an X-ray irradiated strain, Marburg.

Bacillus subtilis subsp. subtilis str. 168

PRJNA76

2003-05-06T00:00:00Z

Industrial producer of starch-based acetone, butanol, and ethanol.

<p> <i><B>Clostridium acetobutylicum</i> strain ATCC 824</B>. This strain was isolated in 1924 from garden soil in Connecticut, USA, by E. Wyer and L. Rettger. It is one of the best studied solventogenic clostridia. The strain has been shown to be closely related to the historical Weizmann strain. It can utilize a broad range of mono- and disaccharides, starches, other substrates such as pectin, xylan, inulin and others. Solventogenic metabolic pathways of this strain have been elucidated. Most of the genes involved in solventogenesis are located on the megaplasmid pSOL1. The strain has been extensively studied from the physiological and bioengineering points of view, genetic systems have been developed that allow genes to be manipulated and solvent-tolerant and solvent-overproducing strains has been engineered.

Clostridium acetobutylicum ATCC 824

PRJNA77

2002-11-22T00:00:00Z

Etiological agent of antibiotic-associated diarrhea and pseudomembraneous colitis.

<p> <i><b>Clostridium difficile</i> strain 630</b>. This strain is the epidemic type X variant that has been extensively studied in research and clinical laboratories. It produces both toxin A, and B.

Clostridioides difficile 630

PRJNA78

2006-09-20T00:00:00Z

Causative agent of gas gangrene.

<b><i>Clostridium</b></i>. This genus comprises about 150 metabolically diverse species of anaerobes that are ubiquitous in virtually all anoxic habitats where organic compounds are present, including soils, aquatic sediments and the intestinal tracts of animals and humans. Characteristic of clostridia is the shape of their cells that resembles a drumstick or spindle ('kloster' is Greek for 'spindle'). This shape is attributed to the presence of endospores that develop under conditions unfavorable for vegetative growth and distend single cells terminally or sub-terminally. The endospores of many species are extremely sturdy and survive extended boiling in water and exposure to air. Spores germinate under conditions favorable for vegetative growth, such as anaerobiosis and presence of organic substrates. From the evolutionary perspective, clostridia are considered to be the most ancient bacteria. It is believed that present day <i>Mollicutes</i> (<i>Eubacteria</i>) have evolved regressively (i.e., by genome reduction) from gram-positive clostridia-like ancestors with a low GC content in DNA. Several species of clostridia (e.g., <i>C. perfringens</i>, <i>C. botulinum</i>, <i>C. tetani</i>) are known opportunistic toxin-producing pathogens in animals and humans. Some species are capable of producing organic solvents (acetone, ethanol, etc,), molecular hydrogen and other useful compounds. There are also species that can fix molecular nitrogen and thus are important participants in biological turnaround of nitrogen compounds in nature. <p> <i><b>Clostridium perfringens</i></b>. This organism is a causative agent of a wide spectrum of necrotic enterotoxicoses. In humans it is responsible for such diseases as gas gangrene (clostridial myonecrosis), food poisoning, necrotizing enterocolitis of infants and enteritis necroticans (pigbel). It also causes such animal diseases as lamb dysentery, ovine enterotoxemia (struck), pulpy kidney disease in lambs and other enterotoxemias in lambs and calves. <p> The bacterium is one of the most widely distributed pathogens in nature. It is commonly found in the environment (soil, sewage) and in the animal and human gastrointestinal tract as a member of the normal microflora. It is a fast growing (generation time 8-10 min) anaerobic flesh-eater. Active fermentative growth is accompanied by profuse generation of molecular hydrogen and carbon dioxide. Unlike most other clostridia, <i>C. perfringens</i> is non-motile. It is also oxygen tolerant which makes it an easy object to work with in laboratories. Systems for genetic manipulation of <i>C. perfringens</i> have been developed and the species became a model organism in clostridial genetic studies. <p> Known isolates belong to five distinct types (A, B, C, D, and E) that are distinguished based on the specific extracellular toxins they produce. Each of the toxins is responsible for a specific disease syndrome. Type A strains that cause gas gangrene produce toxin alpha (phospholypase C), theta (hemolysin), kappa (collagenase), mu (hyaluronidase), nu (DNAse) and neuraminidase which are all the enzymatic factors aiding the bacterium in invading and destruction of the host tissues. <p> <i><b>Clostridium perfringens</i> str. 13</b>. This strain is a type A isolate from the soil. It can establish gas gangrene in a murine experimental model. <p>

Clostridium perfringens str. 13

PRJNA79

2004-05-11T00:00:00Z

Nitrogen-fixing bacterium and potential bioremediator.

<P><i><b>Clostridium pasteurianum</i> sp. BC1</b>. <i>Clostridium pasteurianum</i> sp. BC1 was isolated from coal-cleaning residues. It is a potential candidate for ameliorating radionuclide contamination at DOE sites as it has biochemical pathways that can convert water soluble uranyl (VI) ion, to a less soluble form of this element, U(IV).

Clostridium pasteurianum BC1

PRJNA80

2013-05-06T00:00:00Z

Causative agent of tetanus.

<p> <I><B>Clostridium tetani</I> strain E88</B>. This strain is a virulent nonsporulating variant of strain Massachusetts used in vaccine production.

Clostridium tetani E88

PRJNA81

2003-02-04T00:00:00Z

Commercially available strain used for formula, yogurt, and fluid milk production

<P> <B><I>Lactobacillus acidophilus</I> strain NCFM</B>. This organism is a normal inhabitant of the human intestinal tract. This strain was isolated from a human in 1970 and characterized at North Caroline State University. It is commercially available from Rhodia Inc., and is used for formula, yogurt, and fluid milk production.

Lactobacillus acidophilus NCFM

PRJNA82

2005-01-27T00:00:00Z

Major homofermentative Lactobacillus in human intestinal tract

<P> <B><I>Lactobacillus gasseri</I> ATCC 33323</B>. <I>Lactobacillus gasseri</I> ATCC 33323 is a human isolate and is the type strain. This organism has been shown to have probiotic activities such as production of bacteriocins, macrophage stimulation and adherence to intestinal tissues.

Lactobacillus gasseri ATCC 33323 = JCM 1131

PRJNA84

2006-10-13T00:00:00Z

Opportunistic pathogen that causes important food-born disease

<P> <B><I>Listeria monocytogenes</I> strain 4b F2365</B>. This strain was isolated in 1985 in California, USA, during an outbreak of listeriosis among patients with AIDS. The strain is of serotype 4b and was isolated from a cheese product that caused the outbreak.

Listeria monocytogenes serotype 4b str. F2365

PRJNA85

2004-04-30T00:00:00Z

Nonpathogenic as compared to Listeria monocytogenes

<P><B><I>Listeria innocua</I> strain Clip11262</B>. This strain is serovar 6a and is used for heterologous expression of <I>Listeria monocytogenes</I> genes. This bacterium lacks the virulence gene regulator, PrfA, that is present in <I>Listeria monocytogenes</I> and is responsible for regulation of many virulence genes in the genome.

Listeria innocua Clip11262

PRJNA86

2003-05-06T00:00:00Z

Causative agent of diphtheria.

<p><b><i>Corynebacterium diphtheriae</i></b> biotype <b><i>gravis</i></b> strain <b>NCTC13129</b>. This strain was isolated in 1997 from the pharyngeal membrane of a 72-year-old unimmunized UK female with clinical diphtheria acquired during a short Baltic cruise. Knowing the genetic sequence of this modern strain is important for understanding how to successfully treat the disease that has recently started breaking out in the Eastern Europe.

Corynebacterium diphtheriae NCTC 13129

PRJNA87

2003-11-10T00:00:00Z

Causative agent of mycobacterial disease in children, the aged, and in immunocompromised individuals.

<p> <b><i>Mycobacterium avium</I> strain 104</b></i>. This strain is a common representative of the species complex. It was derived from an AIDS patient and has been characterized for virulence in the murine model of low-dose aerosol infection in that it could colonize the lung, proliferate within the tissue and disseminate to other organs. This strain will be used for comparative analysis with other <I>Mycobacterium</I> species.

Mycobacterium avium 104

PRJNA88

2006-11-20T00:00:00Z

Causative agent of bovine tuberculosis.

<i><b>Mycobacterium bovis</i> subsp. <I> bovis</I> strain AF2122/97</B>. This strain is a fully virulent strain that was isolated in 1997 in the UK from a cow suffering necrotic lesions in lung and bronchomediastinal lymph nodes. The strain was also reported to infect and persist in badgers that are considered to be a significant source of bovine infection.

Mycobacterium tuberculosis variant bovis AF2122/97

PRJNA89

2003-06-13T00:00:00Z

Causative agent of human leprosy.

<p><i><b>Mycobacterium leprae</i> strain TN</b>. This strain (TN) was passaged through an armadillo in Tamil Nadu, India, and is the only strain of this species that has been successfully produced in quantities large enough for sequencing and biochemical analyses as the nine-banded armadillo was used as a surrogate host.

Mycobacterium leprae TN strain:TN

PRJNA90

2003-05-06T00:00:00Z

Causative agent of Johne's disease, or paratuberculosis, a chronic severe intestinal infection.

<p> <i><b>Mycobacterium avium</i> subsp. <i>paratuberculosis</i></b>. This organism is a slowly growing species, with doubling times of around 22-24 hours. One of the important diagnostic features of this bacterium is that its growth in laboratory settings depends on the presence of mycobactin J, a natural siderophore. This bacterium is not common in the environment, and is predominantly found as an intracellular parasite. It causes a chronic granulomatous enteritis termed Johne's disease or paratuberculosis. The desease affects domestic and free-ranging ruminants, but has also been reported in primates, rabbits, stoats and foxes. The usually fatal disease is characterized by weight loss and diarrhea, after a long pre-clinical phase. Treatment is ineffective and economically impracticable. Paratuberculosis in domestic livestock entails significant economic losses in the dairy industry totaling $1.5 billion annually. Several reports suggest a role for this organism in the etiology of Crohn's disease, a severe inflammatory bowel disease in humans. <p> <i><b>Mycobacterium avium</i> subsp. <i>paratuberculosis</i> strain K-10</b>. This strain was isolated from a dairy herd in Wisconsin in the 1970's by investigators from the USDA National Animal Disease Center. It is an extensively studied low passage clinical strain and is amenable to genetic manipulation.

Mycobacterium avium subsp. paratuberculosis K-10 strain:k10

PRJNA91

2004-01-30T00:00:00Z

Generally non-pathogenic mycobacterium capable of causing soft tissue lesions.

<p><b><i>Mycobacterium smegmatis</i> strain MC2 155</b>. This strain (MC2 155) is a mutant of <i>M. smegmatis</i>. It was isolated in 1990. Unlike other strains of this species, MC2 can be 10 to 100 thousand times more efficiently transformed with plasmid vectors using electroporation than the parental strain and thus is invaluable in analysis of mycobacterial gene function, expression and replication.

Mycolicibacterium smegmatis MC2 155

PRJNA92

2006-11-20T00:00:00Z

The wild-type strain for the species, used for comparative genomics.

<p> <b><i>Streptomyces ambofaciens</i> strain ATCC 23877</b>. This is the wild-type and the best studied strain of the species. In addition to netropsin and spiramycin, this strain has been shown, based on genomic data reconfirmed experimentally, to produce a novel angucycline-like polyketide antibiotic.

Streptomyces ambofaciens ATCC 23877

PRJNA93

2015-08-17T00:00:00Z

Thermophilic organism found in decaying organic matter.

<P><i><b>Thermobifida fusca</i> strain YX</b>. This strain is one of the original isolates of <i>T. fusca</i>.

Thermobifida fusca YX strain:YX

PRJNA94

2005-08-08T00:00:00Z

Causative agent of Whipple's disease.

<b><I>Tropheryma whipplei</I> str. Twist</b>. This is the type strain for the species, and is used for comparative genome analysis.

Tropheryma whipplei str. Twist

PRJNA95

2003-02-24T00:00:00Z

Causative agent of polyarthritis and septicemia in goats, sheep and cows

Mycoplasma capricolum

PRJNA96

Causative agent of a wide range of urogenital and respiratory tract infections

<p> <b><i>Mycoplasma genitalium</i> strain G-37</b>. This strain was isolated as a urethral specimen from a male patient with nongonococcal urethritis. This is the type strain for the species and is used for comparative genomics.

Mycoplasmoides genitalium G37

PRJNA97

2002-11-25T00:00:00Z

Etiologic agent of tracheobronchitis and atypical pneumonia in older children and young adults.

<p> <i><b>Mycoplasma pneumoniae</i> strain M129 ATCC29342</b>. This strain is a clinical isolate from a patient with atypical pneumonia. <p>

Mycoplasmoides pneumoniae M129

PRJNA99

2002-12-02T00:00:00Z

Etiologic agent of murine respiratory and genital mycoplasmosis.

<p> <b><i>Mycoplasma pulmonis</i> strain UAB CTIP</b>. This is a popular and well-studied laboratory strain. The respiratory disease it causes is one of the the most important pathologies in laboratory rats and mice, and thus a good model for studying mycoplasmal infections. <p>

Mycoplasmopsis pulmonis UAB CTIP

PRJNA100

2003-05-06T00:00:00Z

Causes a wide range of infections of the urogenital or respiratory tracts

<p><B><I>Ureaplasma parvum</I> serovar 3 str. ATCC 700970</B>. <I>Ureaplasma parvum</I> serovar 3 is the serovar most commonly isolated from humans and this strain was obtained by E. Freundt at the Institue of Medical Microbiology, University of Aarhus, Aarhus, Denmark.

Ureaplasma parvum serovar 3 str. ATCC 700970

PRJNA101

2003-07-17T00:00:00Z

Methane-producing thermophilic archeon

<P><I><B>Methanocaldococcus jannaschii</I> DSM 2661</B>. <I>Methanocaldococcus jannaschii</I> DSM 2661 was isolated from a hydrothermal vent in the east Pacific Rise and is the type strain for the species.

Methanocaldococcus jannaschii DSM 2661

PRJNA102

2004-06-02T00:00:00Z

Anaerobic methane-producing archeon

<P><I><B>Methanosarcina barkeri</I> strain fusaro</B>. <I>Methanosarcina barkeri</I> strain Fusaro was isolated from mud samples taken from the freshwater lake, Lago del Fusaro near Naples, Italy.

Methanosarcina barkeri str. Fusaro

PRJNA103

2005-08-12T00:00:00Z

Hyperthermophilic sulfate-reducing archaeon

<P> <I><B>Archaeoglobus fulgidus</I> strain VC-16</B>. This is the type strain (DSM 4304) of the Archaeoglobales, and was isolated from a geothermally heated sea floor at Vulcano Island, Italy. Doubling time is four hours under optimal conditions. The organism is an autotrophic or organotrophic sulfate/sulfite respirer. An additional distinguishing characteristic is blue-green fluorescence at 420 nm.

Archaeoglobus fulgidus DSM 4304

PRJNA104

2001-01-09T00:00:00Z

Chemoheterotrophic obligate extreme halophilic archeon

<P> <I><B>Haloarcula marismortui</I> ATCC 43049</B>. This organism was isolated from the Dead Sea and will provide information on the proteins necessary for adaptation to a high salt environment.

Haloarcula marismortui ATCC 43049

PRJNA105

2004-11-02T00:00:00Z

Chemoheterotrophic obligate extreme halophilic archeon

<P> <I><B>Halobacterium salinarium</I> strain R1</B/>. <I>Halobacterium salinarium</I> strain R1(DSM 671) forms translucent red colonies as opposed to the opaque pink colonies formed by <I>Halobacterium salinarium</I> NRL. Strain R1 has no gas vacuoles and will be used for comparison with other <I>Halobacterium</I> species.

Halobacterium salinarum R1 strain:R1

PRJNA106

2008-02-12T00:00:00Z

Hyperthermophilic acidophilic sulfur-metabolizing archeon

<P><I><B>Sulfolobus solfataricus</I> strain P2</B>. This strain is a model organism for studying crenarchaeal biology and will be used for comparative analysis.

Saccharolobus solfataricus P2 strain:P2

PRJNA108

2002-11-25T00:00:00Z

Thermophilic acidophilic archaea

<P><I><B>Thermoplasma acidophilum</I> strain DSM 1728</B>. This strain is the type strain for this species, and was isolated from a burning refuse coal pile from the Friar Tuck mine in Indiana, USA.

Thermoplasma acidophilum DSM 1728

PRJNA110

2003-05-06T00:00:00Z

Hyperthermophilic organism that shows extensive horizontal gene transfer from archaea

<P><B><I>Thermotoga maritima</I> strain MSB8</B>. This hyperthermophilic organism was originally isolated from a geothermal marine area near Vulcano, Italy. Strain MSB8 is the type strain. It is representative of a very deep branch of eubacteria and a very large portion of the genome, 24% of all ORFs, is similar to archaeal genes, suggesting horizontal gene transfer, a hypothesis supported by the fact that many regions of the chromosome containing these genes have a significantly different composition as compared to the rest of the genome. This organism appears to live in a rich environment as it encodes a large number of transporters, both for import and export, of complex substrates such as carbohydrates, including a type II secretion system that may be used to export extracellular enzymes for degradation of biopolymers.

Thermotoga maritima MSB8

PRJNA111

2001-01-09T00:00:00Z

Porphyra yezoensis EST project

To understand the genetic system in red algae, large scale EST analysis of <b><i>Porphyra yezoensis</i></b> has been going on at the <b>Kazusa DNA Research Institute</b>. Large number of sequences have currently been generated from both gametophytic and sporophytic tissues of P. yezoensis Ueda (strain TU-1). The sequence data is available from the <a href="http://www.kazusa.or.jp/en/plant/porphyra/EST/">Kazusa</a> website.

Neopyropia yezoensis strain:TU-1

PRJNA113

Emiliania huxleyi EST sequencing projects

<p> Large scale EST sequencing of <i>Emiliania huxleyi</i> is being carried out at <b>California State University, San Marcos</b>. <br> In addition, an EST project is also in progress at the <b>University of Iowa</b> with an aim to understand the process of eukaryotic endosymbiosis.

Emiliania huxleyi strain:1516

PRJNA114

Alexandrium tamarense EST project

To understand the process of endosymbiosis, there is a Joint NSF-USDA funded project to sequence large scale ESTs from <i>Alexandrium tamarense</i> and <i>Emiliania huxleyi</i> which is the source of plastid for <i>A. tamarense</i>. Sequencing is being carried out at the University of Iowa.

Alexandrium tamarense

PRJNA115

Refseq project

<p> The reference sequence assembly for Arabidopsis is created by NCBI based on the genome data provided by <a href="http://www.arabidopsis.org/">The Arbidopsis Information Resource (TAIR)</a>. Functional annotation is continuously being updated, last updated in February, 2014.</p> Mitochondrial genome of Arabidopsis was sequenced at the <b>Institut fur Genbiologische Forschung, Berlin, Germany</b> and the chloroplast genome was sequenced at the <b>Kazusa DNA Research Institute, Japan</b> <p>

Arabidopsis thaliana

PRJNA116

2011-05-05T00:00:00Z

Glycine max Map

Three maps are presented. Two are composite maps constructed by integrating the mapping data from many mapping endeavors that use three mapping populations: the USDA/Iowa State University population, the University of Utah RIL population and the University of Nebraska NIL population. The third map is the result of a concerted effort to develop SSR probes and map them in the mapping populations underlying the composite maps plus two other populations.

Glycine max

PRJNA117

chloroplast genome completely sequenced

<p> <i>Medicago truncatula</i> chloroplast genome was sequenced at the University of Oklahoma in partnership with the noble foundation. The DNA sequence consists of one contiguous 124,039 base pair circle. Artificially linearizing the genome shows Medicago chloroplast genomic sequence to be co-linear with the arabadopsis, tobacco and most other chloroplast genomes. Semi-automated <a href="http://www.genome.ou.edu/medicago_chloroplast/med_chloro_art.html">annotation</a> of the chloroplast genome using Web-Artemis is available.

Medicago truncatula

PRJNA118

Sequencing of the tomato genome by the international consortium

<p>Sequencing of the tomato genome will be done by an international consortium of researchers as part of the Solanaceae Genomics Project. The plan is to sequence the gene rich regions of all 12 chromosomes on BAC by BAC basis and annotate it. The US has agreed to sequence chromosomes 1 and 10 with the majority of the funding by the NSF and the USDA Plant Genome program. Other participating member countries are Korea (chromosome 2), China (chromosome 3 and 11), UK (chromosome 4), India (chromosome 5), The Netherlands (chromosome 6), France (chromosome 7), Japan (chromosome 8) Spain (chromosome 9) and Italy (chromosome 12).

Solanum lycopersicum cultivar:Heinz 1706

PRJNA119

2010-12-10T00:00:00Z

Oat mapping projects

Despite difficulties associated with mapping a large hexaploid genome with numerous chromosomal rearrangements, various diploid and hexaploid maps have been generated for oats. All the data is maintained by GrainGenes database which is supported by the USDA-ARS Plant Genome Research Program.

Avena sativa

PRJNA120

Barley genetic maps

Barley mapping data is being maintained by GrainGenes. Currently twenty-five maps are available at NCBI.

Hordeum vulgare maps

PRJNA121