Publications by authors named "Jim Bristow"

53 Publications

Complete Genome sequence of Burkholderia phymatum STM815(T), a broad host range and efficient nitrogen-fixing symbiont of Mimosa species.

Stand Genomic Sci 2014 Jun 25;9(3):763-74. Epub 2014 Mar 25.

Univ Massachussets, MA, USA.

Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815(T), was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp).
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http://dx.doi.org/10.4056/sigs.4861021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4148976PMC
June 2014

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.

PLoS Genet 2011 Jun 9;7(6):e1002070. Epub 2011 Jun 9.

USDA-Agricultural Research Service, Purdue University, West Lafayette, Indiana, United States of America.

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed "mesosynteny" is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors.
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http://dx.doi.org/10.1371/journal.pgen.1002070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111534PMC
June 2011

Complete genome sequence of Marivirga tractuosa type strain (H-43).

Stand Genomic Sci 2011 Apr;4(2):154-62

Marivirga tractuosa (Lewin 1969) Nedashkovskaya et al. 2010 is the type species of the genus Marivirga, which belongs to the family Flammeovirgaceae. Members of this genus are of interest because of their gliding motility. The species is of interest because representative strains show resistance to several antibiotics, including gentamicin, kanamycin, neomycin, polymixin and streptomycin. This is the first complete genome sequence of a member of the family Flammeovirgaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,511,574 bp long chromosome and the 4,916 bp plasmid with their 3,808 protein-coding and 49 RNA genes are a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.1623941DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111994PMC
April 2011

Complete genome sequence of Arthrobacter phenanthrenivorans type strain (Sphe3).

Stand Genomic Sci 2011 Apr;4(2):123-30

Arthrobacter phenanthrenivorans is the type species of the genus, and is able to metabolize phenanthrene as a sole source of carbon and energy. A. phenanthrenivorans is an aerobic, non-motile, and Gram-positive bacterium, exhibiting a rod-coccus growth cycle which was originally isolated from a creosote polluted site in Epirus, Greece. Here we describe the features of this organism, together with the complete genome sequence, and annotation.
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http://dx.doi.org/10.4056/sigs.1393494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111998PMC
April 2011

Complete genome sequence of Desulfarculus baarsii type strain (2st14).

Stand Genomic Sci 2010 Nov 20;3(3):276-84. Epub 2010 Nov 20.

Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006 is the type and only species of the genus Desulfarculus, which represents the family Desulfarculaceae and the order Desulfarculales. This species is a mesophilic sulfate-reducing bacterium with the capability to oxidize acetate and fatty acids of up to 18 carbon atoms completely to CO(2). The acetyl-CoA/CODH (Wood-Ljungdahl) pathway is used by this species for the complete oxidation of carbon sources and autotrophic growth on formate. The type strain 2st14(T) was isolated from a ditch sediment collected near the University of Konstanz, Germany. This is the first completed genome sequence of a member of the order Desulfarculales. The 3,655,731 bp long single replicon genome with its 3,303 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.1243258DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035298PMC
November 2010

Complete genome sequence of Archaeoglobus profundus type strain (AV18).

Stand Genomic Sci 2010 Jun 15;2(3):327-46. Epub 2010 Jun 15.

Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the euryarchaeal class Archaeoglobi, which is currently represented by the single family Archaeoglobaceae, containing six validly named species and two strains ascribed to the genus 'Geoglobus' which is taxonomically challenged as the corresponding type species has no validly published name. All members were isolated from marine hydrothermal habitats and are obligate anaerobes. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member of the class Archaeoglobi. The 1,563,423 bp genome with its 1,858 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.942153DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035285PMC
June 2010

Complete genome sequence of Conexibacter woesei type strain (ID131577).

Stand Genomic Sci 2010 Mar 30;2(2):212-9. Epub 2010 Mar 30.

The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with Conexibacter woesei as the type species of the genus. C. woesei is a representative of a deep evolutionary line of descent within the class Actinobacteria. Strain ID131577(T) was originally isolated from temperate forest soil in Gerenzano (Italy). Cells are small, short rods that are motile by peritrichous flagella. They may form aggregates after a longer period of growth and, then as a typical characteristic, an undulate structure is formed by self-aggregation of flagella with entangled bacterial cells. Here we describe the features of the organism, together with the complete sequence and annotation. The 6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.751339DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035278PMC
March 2010

Complete genome sequence of Segniliparus rotundus type strain (CDC 1076).

Stand Genomic Sci 2010 Mar 30;2(2):203-11. Epub 2010 Mar 30.

Segniliparus rotundus Butler 2005 is the type species of the genus Segniliparus, which is currently the only genus in the corynebacterial family Segniliparaceae. This family is of large interest because of a novel late-emerging genus-specific mycolate pattern. The type strain has been isolated from human sputum and is probably an opportunistic pathogen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Segniliparaceae. The 3,157,527 bp long genome with its 3,081 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.791633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035277PMC
March 2010

Complete genome sequence of Kribbella flavida type strain (IFO 14399).

Stand Genomic Sci 2010 Mar 30;2(2):186-93. Epub 2010 Mar 30.

The genus Kribbella consists of 15 species, with Kribbella flavida (Park et al. 1999) as the type species. The name Kribbella was formed from the acronym of the Korea Research Institute of Bioscience and Biotechnology, KRIBB. Strains of the various Kribbella species were originally isolated from soil, potato, alum slate mine, patinas of catacombs or from horse racecourses. Here we describe the features of K. flavida together with the complete genome sequence and annotation. In addition to the 5.3 Mbp genome of Nocardioides sp. JS614, this is only the second completed genome sequence of the family Nocardioidaceae. The 7,579,488 bp long genome with its 7,086 protein-coding and 60 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.731321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035274PMC
March 2010

Complete genome sequence of Spirosoma linguale type strain (1).

Stand Genomic Sci 2010 Mar 30;2(2):176-85. Epub 2010 Mar 30.

Spirosoma linguale Migula 1894 is the type species of the genus. S. linguale is a free-living and non-pathogenic organism, known for its peculiar ringlike and horseshoe-shaped cell morphology. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is only the third completed genome sequence of a member of the family Cytophagaceae. The 8,491,258 bp long genome with its eight plasmids, 7,069 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.741334DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035282PMC
March 2010

Complete genome sequence of Nakamurella multipartita type strain (Y-104).

Stand Genomic Sci 2010 Mar 30;2(2):168-75. Epub 2010 Mar 30.

Nakamurella multipartita (Yoshimi et al. 1996) Tao et al. 2004 is the type species of the monospecific genus Nakamurella in the actinobacterial suborder Frankineae. The nonmotile, coccus-shaped strain was isolated from activated sludge acclimated with sugar-containing synthetic wastewater, and is capable of accumulating large amounts of polysaccharides in its cells. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Nakamurellaceae. The 6,060,298 bp long single replicon genome with its 5415 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.721316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035273PMC
March 2010

Complete genome sequence of Geodermatophilus obscurus type strain (G-20).

Stand Genomic Sci 2010 Mar 30;2(2):158-67. Epub 2010 Mar 30.

Geodermatophilus obscurus Luedemann 1968 is the type species of the genus, which is the type genus of the family Geodermatophilaceae. G. obscurus is of interest as it has frequently been isolated from stressful environments such as rock varnish in deserts, and as it exhibits interesting phenotypes such as lytic capability of yeast cell walls, UV-C resistance, strong production of extracellular functional amyloid (FuBA) and manganese oxidation. This is the first completed genome sequence of the family Geodermatophilaceae. The 5,322,497 bp long genome with its 5,161 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.711311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035280PMC
March 2010

Complete genome sequence of Sulfurospirillum deleyianum type strain (5175).

Stand Genomic Sci 2010 Mar 24;2(2):149-57. Epub 2010 Mar 24.

Sulfurospirillum deleyianum Schumacher et al. 1993 is the type species of the genus Sulfurospirillum. S. deleyianum is a model organism for studying sulfur reduction and dissimilatory nitrate reduction as an energy source for growth. Also, it is a prominent model organism for studying the structural and functional characteristics of cytochrome c nitrite reductase. Here, we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the genus Sulfurospirillum. The 2,306,351 bp long genome with its 2,291 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.671209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035281PMC
March 2010

Complete genome sequence of Haliangium ochraceum type strain (SMP-2).

Stand Genomic Sci 2010 Jan 28;2(1):96-106. Epub 2010 Jan 28.

Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the myxococcal family 'Haliangiaceae'. Members of the genus Haliangium are the first halophilic myxobacterial taxa described. The cells of the species follow a multicellular lifestyle in highly organized biofilms, called swarms, they decompose bacterial and yeast cells as most myxobacteria do. The fruiting bodies contain particularly small coccoid myxospores. H. ochraceum encodes the first actin homologue identified in a bacterial genome. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the myxococcal suborder Nannocystineae, and the 9,446,314 bp long single replicon genome with its 6,898 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.69.1277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035250PMC
January 2010

Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034).

Stand Genomic Sci 2010 Feb 28;2(1):87-95. Epub 2010 Feb 28.

Chitinophaga pinensis Sangkhobol and Skerman 1981 is the type strain of the species which is the type species of the rapidly growing genus Chitinophaga in the sphingobacterial family 'Chitinophagaceae'. Members of the genus Chitinophaga vary in shape between filaments and spherical bodies without the production of a fruiting body, produce myxospores, and are of special interest for their ability to degrade chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family 'Chitinophagaceae', and the 9,127,347 bp long single replicon genome with its 7,397 protein-coding and 95 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.661199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035255PMC
February 2010

Complete genome sequence of Veillonella parvula type strain (Te3).

Stand Genomic Sci 2010 Jan 28;2(1):57-65. Epub 2010 Jan 28.

Veillonella parvula (Veillon and Zuber 1898) Prévot 1933 is the type species of the genus Veillonella in the family Veillonellaceae within the order Clostridiales. The species V. parvula is of interest because it is frequently isolated from dental plaque in the human oral cavity and can cause opportunistic infections. The species is strictly anaerobic and grows as small cocci which usually occur in pairs. Veillonellae are characterized by their unusual metabolism which is centered on the activity of the enzyme methylmalonyl-CoA decarboxylase. Strain Te3(T), the type strain of the species, was isolated from the human intestinal tract. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the large clostridial family Veillonellaceae, and the 2,132,142 bp long single replicon genome with its 1,859 protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.521107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035260PMC
January 2010

Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022).

Stand Genomic Sci 2010 Jan 28;2(1):49-56. Epub 2010 Jan 28.

Sphaerobacter thermophilus Demharter et al. 1989 is the sole and type species of the genus Sphaerobacter, which is the type genus of the family Sphaerobacteraceae, the order Sphaerobacterales and the subclass Sphaerobacteridae. Phylogenetically, it belongs to the genomically little studied class of the Thermomicrobia in the bacterial phylum Chloroflexi. Here, the genome of strain S 6022(T) is described which is an obligate aerobe that was originally isolated from an aerated laboratory-scale fermentor that was pulse fed with municipal sewage sludge. We describe the features of this organism, together with the complete genome and annotation. This is the first complete genome sequence of the thermomicrobial subclass Sphaerobacteridae, and the second sequence from the chloroflexal class Thermomicrobia. The 3,993,764 bp genome with its 3,525 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.601105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035262PMC
January 2010

Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)).

Stand Genomic Sci 2010 Jan 28;2(1):38-48. Epub 2010 Jan 28.

Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H(2) and a limited range of organic substrates, which are incompletely oxidized to acetate and CO(2), for growth. The type strain HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.581048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035252PMC
January 2010

Complete genome sequence of Streptosporangium roseum type strain (NI 9100).

Stand Genomic Sci 2010 Jan 28;2(1):29-37. Epub 2010 Jan 28.

Streptosporangium roseum Crauch 1955 is the type strain of the species which is the type species of the genus Streptosporangium. The 'pinkish coiled Streptomyces-like organism with a spore case' was isolated from vegetable garden soil in 1955. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Streptosporangiaceae, and the second largest microbial genome sequence ever deciphered. The 10,369,518 bp long genome with its 9421 protein-coding and 80 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.631049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035251PMC
January 2010

Complete genome sequence of Gordonia bronchialis type strain (3410).

Stand Genomic Sci 2010 Jan 28;2(1):19-28. Epub 2010 Jan 28.

Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.611106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035257PMC
January 2010

Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA).

Stand Genomic Sci 2010 Jan 28;2(1):9-18. Epub 2010 Jan 28.

Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family 'Alicyclobacillaceae'. A. acidocaldarius is a free-living and non-pathogenic organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family 'Alicyclobacillaceae'. The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.591104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035248PMC
January 2010

Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07).

Stand Genomic Sci 2010 Jan 28;2(1):1-8. Epub 2010 Jan 28.

Xylanimonas cellulosilytica Rivas et al. 2003 is the type species of the genus Xylanimonas of the actinobacterial family Promicromonosporaceae. The species X. cellulosilytica is of interest because of its ability to hydrolyze cellulose and xylan. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the large family Promicromonosporaceae, and the 3,831,380 bp long genome (one chromosome plus an 88,604 bp long plasmid) with its 3485 protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.571102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035249PMC
January 2010

The genome sequence of Methanohalophilus mahii SLP(T) reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments.

Archaea 2010 Dec 23;2010:690737. Epub 2010 Dec 23.

DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany.

Methanohalophilus mahii is the type species of the genus Methanohalophilus, which currently comprises three distinct species with validly published names. Mhp. mahii represents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLP(T) was isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of the Genomic Encyclopedia of Bacteria and Archaea project. A comparison of the reconstructed energy metabolism in the halophilic species Mhp. mahii with other representatives of the Methanosarcinaceae reveals some interesting differences to freshwater species.
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http://dx.doi.org/10.1155/2010/690737DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3017947PMC
December 2010

Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma.

J Allergy Clin Immunol 2011 Feb 30;127(2):372-381.e1-3. Epub 2010 Dec 30.

Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California, San Francisco, Calif, USA.

Background: Improvement in lung function after macrolide antibiotic therapy has been attributed to reduction in bronchial infection by specific bacteria. However, the airway might be populated by a more diverse microbiota, and clinical features of asthma might be associated with characteristics of the airway microbiota present.

Objective: We sought to determine whether relationships exist between the composition of the airway bacterial microbiota and clinical features of asthma using culture-independent tools capable of detecting the presence and relative abundance of most known bacteria.

Methods: In this pilot study bronchial epithelial brushings were collected from 65 adults with suboptimally controlled asthma participating in a multicenter study of the effects of clarithromycin on asthma control and 10 healthy control subjects. A combination of high-density 16S ribosomal RNA microarray and parallel clone library-sequencing analysis was used to profile the microbiota and examine relationships with clinical measurements.

Results: Compared with control subjects, 16S ribosomal RNA amplicon concentrations (a proxy for bacterial burden) and bacterial diversity were significantly higher among asthmatic patients. In multivariate analyses airway microbiota composition and diversity were significantly correlated with bronchial hyperresponsiveness. Specifically, the relative abundance of particular phylotypes, including members of the Comamonadaceae, Sphingomonadaceae, Oxalobacteraceae, and other bacterial families were highly correlated with the degree of bronchial hyperresponsiveness.

Conclusion: The composition of bronchial airway microbiota is associated with the degree of bronchial hyperresponsiveness among patients with suboptimally controlled asthma. These findings support the need for further functional studies to examine the potential contribution of members of the airway microbiota in asthma pathogenesis.
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http://dx.doi.org/10.1016/j.jaci.2010.10.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037020PMC
February 2011

Biocorrosive thermophilic microbial communities in Alaskan North Slope oil facilities.

Environ Sci Technol 2009 Oct;43(20):7977-84

Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, USA.

Corrosion of metallic oilfield pipelines by microorganisms is a costly but poorly understood phenomenon, with standard treatment methods targeting mesophilic sulfate-reducing bacteria. In assessing biocorrosion potential at an Alaskan North Slope oil field, we identified thermophilic hydrogen-using methanogens, syntrophic bacteria, peptide- and amino acid-fermenting bacteria, iron reducers, sulfur/thiosulfate-reducing bacteria, and sulfate-reducing archaea. These microbes can stimulate metal corrosion through production of organic acids, CO2, sulfur species, and via hydrogen oxidation and iron reduction, implicating many more types of organisms than are currently targeted. Micromolar quantities of putative anaerobic metabolites of C1-C4 n-alkanes in pipeline fluids were detected, implying that these low molecular weight hydrocarbons, routinely reinjected into reservoirs for oil recovery purposes, are biodegraded and can provide biocorrosive microbial communities with an important source of nutrients.
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http://dx.doi.org/10.1021/es9013932DOI Listing
October 2009

Complete genome sequence of Pirellula staleyi type strain (ATCC 27377).

Stand Genomic Sci 2009 Dec 30;1(3):308-16. Epub 2009 Dec 30.

Pirellula staleyi Schlesner and Hirsch 1987 is the type species of the genus Pirellula of the family Planctomycetaceae. Members of this pear- or teardrop-shaped bacterium show a clearly visible pointed attachment pole and can be distinguished from other Planctomycetes by a lack of true stalks. Strains closely related to the species have been isolated from fresh and brackish water, as well as from hypersaline lakes. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the order Planctomyces and only the second sequence from the phylum Planctobacteria/Planctomycetes. The 6,196,199 bp long genome with its 4773 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.51657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035237PMC
December 2009

Complete genome sequence of Streptobacillus moniliformis type strain (9901).

Stand Genomic Sci 2009 Dec 30;1(3):300-7. Epub 2009 Dec 30.

Streptobacillus moniliformis Levaditi et al. 1925 is the type and sole species of the genus Streptobacillus, and is of phylogenetic interest because of its isolated location in the sparsely populated and neither taxonomically nor genomically much accessed family 'Leptotrichiaceae' within the phylum Fusobacteria. The 'Leptotrichiaceae' have not been well characterized, genomically or taxonomically. S. moniliformis,is a Gram-negative, non-motile, pleomorphic bacterium and is the etiologic agent of rat bite fever and Haverhill fever. Strain 9901(T), the type strain of the species, was isolated from a patient with rat bite fever. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is only the second completed genome sequence of the order Fusobacteriales and no more than the third sequence from the phylum Fusobacteria. The 1,662,578 bp long chromosome and the 10,702 bp plasmid with a total of 1511 protein-coding and 55 RNA genes are part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.48727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035246PMC
December 2009

Complete genome sequence of Halomicrobium mukohataei type strain (arg-2).

Stand Genomic Sci 2009 Nov 22;1(3):270-7. Epub 2009 Nov 22.

Halomicrobium mukohataei (Ihara et al. 1997) Oren et al. 2002 is the type species of the genus Halomicrobium. It is of phylogenetic interest because of its isolated location within the large euryarchaeal family Halobacteriaceae. H. mukohataei is an extreme halophile that grows essentially aerobically, but can also grow anaerobically under a change of morphology and with nitrate as electron acceptor. The strain, whose genome is described in this report, is a free-living, motile, Gram-negative euryarchaeon, originally isolated from Salinas Grandes in Jujuy, Andes highlands, Argentina. Its genome contains three genes for the 16S rRNA that differ from each other by up to 9%. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence from the poorly populated genus Halomicrobium, and the 3,332,349 bp long genome (chromosome and one plasmid) with its 3416 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.42644DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035239PMC
November 2009

Complete genome sequence of Jonesia denitrificans type strain (Prevot 55134).

Stand Genomic Sci 2009 Nov 22;1(3):262-9. Epub 2009 Nov 22.

Jonesia denitrificans (Prevot 1961) Rocourt et al. 1987 is the type species of the genus Jonesia, and is of phylogenetic interest because of its isolated location in the actinobacterial suborder Micrococcineae. J. denitrificans is characterized by a typical coryneform morphology and is able to form irregular nonsporulating rods showing branched and club-like forms. Coccoid cells occur in older cultures. J. denitrificans is classified as a pathogenic organism for animals (vertebrates). The type strain whose genome is described here was originally isolated from cooked ox blood. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the genus for which a complete genome sequence is described. The 2,749,646 bp long genome with its 2558 protein-coding and 71 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
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http://dx.doi.org/10.4056/sigs.41646DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035236PMC
November 2009