Markus Göker

Publications of Markus Göker

• Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics.

  Authors: Lea A I Vaas, Johannes Sikorski, Victoria Michael, Markus Göker, Hans-Peter Klenk

  PloS one. 01/2012; 7(4):e34846.

  The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This techniqueThe Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This technique targets the object of natural selection itself, the phenotype, whereas previously addressed '-omics' techniques merely study components that finally contribute to it. The recording of respiration over time, however, adds a longitudinal dimension to the data. To optimally exploit this information, it must be extracted from the shapes of the recorded curves and displayed in analogy to conventional growth curves. The free software environment R was explored for both visualizing and fitting of PM respiration curves. Approaches using either a model fit (and commonly applied growth models) or a smoothing spline were evaluated. Their reliability in inferring curve parameters and confidence intervals was compared to the native OmniLog® PM analysis software. We consider the post-processing of the estimated parameters, the optimal classification of curve shapes and the detection of significant differences between them, as well as practically relevant questions such as detecting the impact of cultivation times and the minimum required number of experimental repeats. We provide a comprehensive framework for data visualization and parameter estimation according to user choices. A flexible graphical representation strategy for displaying the results is proposed, including 95% confidence intervals for the estimated parameters. The spline approach is less prone to irregular curve shapes than fitting any of the considered models or using the native PM software for calculating both point estimates and confidence intervals. These can serve as a starting point for the automated post-processing of PM data, providing much more information than the strict dichotomization into positive and negative reactions. Our results form the basis for a freely available R package for the analysis of PM data.

• Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010.

  Authors: Hans-Peter Klenk, Alla Lapidus, Olga Chertkov, Alex Copeland, Tijana Glavina Del Rio, Matt Nolan, Susan Lucas, Feng Chen, Hope Tice, Jan-Fang Cheng [......] Cynthia D Jeffries, John C Detter, Manfred Rohde, Birte Abt, Rüdiger Pukall, Markus Göker, James Bristow, Victor Markowitz, Philip Hugenholtz, Jonathan A Eisen

  Standards in genomic sciences. 10/2011; 5(1):121-34.

  Bacillus tusciae Bonjour & Aragno 1994 is a hydrogen-oxidizing, thermoacidophilic spore former that lives as a facultative chemolithoautotroph in solfataras. Although 16S rRNA gene sequencing wasBacillus tusciae Bonjour & Aragno 1994 is a hydrogen-oxidizing, thermoacidophilic spore former that lives as a facultative chemolithoautotroph in solfataras. Although 16S rRNA gene sequencing was well established at the time of the initial description of the organism, 16S sequence data were not available and the strain was placed into the genus Bacillus based on limited chemotaxonomic information. Despite the now obvious misplacement of strain T2 as a member of the genus Bacillus in 16S rRNA-based phylogenetic trees, the misclassification remained uncorrected for many years, which was likely due to the extremely difficult, analysis-hampering cultivation conditions and poor growth rate of the strain. Here we provide a taxonomic re-evaluation of strain T2T (= DSM 2912 = NBRC 15312) and propose its reclassification as the type strain of a new species, Kyrpidia tusciae, and the type species of the new genus Kyrpidia, which is a sister-group of Alicyclobacillus. The family Alicyclobacillaceae da Costa and Rainey, 2010 is emended. The 3,384,766 bp genome with its 3,323 protein-coding and 78 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21).

  Authors: Yun-Juan Chang, Miriam Land, Loren Hauser, Olga Chertkov, Tijana Glavina Del Rio, Matt Nolan, Alex Copeland, Hope Tice, Jan-Fang Cheng, Susan Lucas [......] Markus Göker, John C Detter, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, Alla Lapidus

  Standards in genomic sciences. 10/2011; 5(1):97-111.

  Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the orderKtedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum 'Chloroflexi'. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum 'Chloroflexi'. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the genetic redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Complete genome sequence of Tolumonas auensis type strain (TA 4).

  Authors: Olga Chertkov, Alex Copeland, Susan Lucas, Alla Lapidus, Kerrie W Berry, John C Detter, Tijana Glavina Del Rio, Nancy Hammon, Eileen Dalin, Hope Tice [......] Miriam Land, Loren Hauser, Stefan Spring, Manfred Rohde, Nikos C Kyrpides, Natalia Ivanova, Markus Göker, Harry R Beller, Hans-Peter Klenk, Tanja Woyke

  Standards in genomic sciences. 10/2011; 5(1):112-20.

  Tolumonas auensis Fischer-Romero et al. 1996 is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability toTolumonas auensis Fischer-Romero et al. 1996 is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Other than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4(T) is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292 bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008.

• Complete genome sequence of the gliding freshwater bacterium Fluviicola taffensis type strain (RW262).

  Authors: Tanja Woyke, Olga Chertkov, Alla Lapidus, Matt Nolan, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Roxanne Tapia, Cliff Han [......] Romano Mwirichia, Johannes Sikorski, Brian J Tindall, Markus Göker, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, Nikos C Kyrpides

  Standards in genomic sciences. 10/2011; 5(1):21-9.

  Fluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in theFluviicola taffensis O'Sullivan et al. 2005 belongs to the monotypic genus Fluviicola within the family Cryomorphaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of the tree of life. Strain RW262(T) forms a monophyletic lineage with uncultivated bacteria represented in freshwater 16S rRNA gene libraries. A similar phylogenetic differentiation occurs between freshwater and marine bacteria in the family Flavobacteriaceae, a sister family to Cryomorphaceae. Most remarkable is the inability of this freshwater bacterium to grow in the presence of Na(+) ions. All other genera in the family Cryomorphaceae are from marine habitats and have an absolute requirement for Na(+) ions or natural sea water. F. taffensis is the first member of the family Cryomorphaceae with a completely sequenced and publicly available genome. The 4,633,577 bp long genome with its 4,082 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113).

  Authors: Konstantinos Liolios, Johannes Sikorski, Meagan Lu, Matt Nolan, Alla Lapidus, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia [......] Birte Abt, Markus Göker, John C Detter, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, Nikos C Kyrpides

  Standards in genomic sciences. 10/2011; 5(1):30-40.

  Pedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus Pedobacter within the family Sphingobacteriaceae. The species is of interest for its isolated location in the tree ofPedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus Pedobacter within the family Sphingobacteriaceae. The species is of interest for its isolated location in the tree of life. Like other members of the genus P. saltans is heparinolytic. Cells of P. saltans show a peculiar gliding, dancing motility and can be distinguished from other Pedobacter strains by their ability to utilize glycerol and the inability to assimilate D-cellobiose. The genome presented here is only the second completed genome sequence of a type strain from a member of the family Sphingobacteriaceae to be published. The 4,635,236 bp long genome with its 3,854 protein-coding and 67 RNA genes consists of one chromosome, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20).

  Authors: Amrita Pati, Sabine Gronow, Megan Lu, Alla Lapidus, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia [......] Manfred Rohde, Markus Göker, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, Natalia Ivanova

  Standards in genomic sciences. 10/2011; 5(1):41-9.

  Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members arePrevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members are able to cause diseases in the human oral cavity such as periodontitis, root caries and others. Although 77 Prevotella genomes have already been sequenced or are targeted for sequencing, this is only the second completed genome sequence of a type strain of a species within the genus Prevotella to be published. The 3,388,644 bp long genome is assembled in three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Genome sequence of the moderately thermophilic halophile Flexistipes sinusarabici strain (MAS10).

  Authors: Alla Lapidus, Olga Chertkov, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia, Cliff Han, Lynne Goodwin [......] Birte Abt, Stefan Spring, Markus Göker, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, Tanja Woyke

  Standards in genomic sciences. 10/2011; 5(1):86-96.

  Flexistipes sinusarabici Fiala et al. 2000 is the type species of the genus Flexistipes in the family Deferribacteraceae. The species is of interest because of its isolated phylogenetic location in aFlexistipes sinusarabici Fiala et al. 2000 is the type species of the genus Flexistipes in the family Deferribacteraceae. The species is of interest because of its isolated phylogenetic location in a genomically under-characterized region of the tree of life, and because of its origin from a multiply extreme environment; the Atlantis Deep brines of the Red Sea, where it had to struggle with high temperatures, high salinity, and a high concentrations of heavy metals. This is the fourth completed genome sequence to be published of a type strain of the family Deferribacteraceae. The 2,526,590 bp long genome with its 2,346 protein-coding and 53 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Charcoal filter paper improves the viability of cryopreserved filamentous ectomycorrhizal and saprotrophic Basidiomycota and Ascomycota.

  Authors: J Benjamin Stielow, Lea A I Vaas, Markus Göker, Peter Hoffmann, Hans-Peter Klenk

  Mycologia. 09/2011; 104(1):324-30.

  We assessed viability of 18 strains of filamentous ectomycorrhizal and saprotrophic basid-iomycetes and ascomycetes after cryopreservation with a novel technique based on charcoal filter paper stripsWe assessed viability of 18 strains of filamentous ectomycorrhizal and saprotrophic basid-iomycetes and ascomycetes after cryopreservation with a novel technique based on charcoal filter paper strips (CFS). The results indicate that axenic fungal cultures grown on CFS recovered from freezing within a few days, even though none survived cryopreservation by the conventional straw method. Fungal growth on CFS was more vigorous, with morphological differentiations such as rhizomorphs and an increased amount of aerial mycelia compared to the unamended culture media. Accordingly CFS allows the cryopreservation of a wide range of rare and important ectomycorrhizal and saprotrophic fungi, which hitherto were difficult to revive from liquid nitrogen storage with the conventional and widely applied straw technique.

• Complete genome sequence of Rhodospirillum rubrum type strain (S1).

  Authors: A Christine Munk, Alex Copeland, Susan Lucas, Alla Lapidus, Tijana Glavina Del Rio, Kerrie Barry, John C Detter, Nancy Hammon, Sanjay Israni, Sam Pitluck [......] Nikos C Kyrpides, Konstantinos Mavromatis, Paul Richardson, Manfred Rohde, Markus Göker, Hans-Peter Klenk, Yaoping Zhang, Gary P Roberts, Susan Reslewic, David C Schwartz

  Standards in genomic sciences. 07/2011; 4(3):293-302.

  Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rhodospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteobacteria. TheRhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rhodospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteobacteria. The species is of special interest because it is an anoxygenic phototroph that produces extracellular elemental sulfur (instead of oxygen) while harvesting light. It contains one of the most simple photosynthetic systems currently known, lacking light harvesting complex 2. Strain S1(T) can grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed entries, R. rubrum is one of the most intensively studied microbial species, in particular for physiological and genetic studies. Next to R. centenum strain SW, the genome sequence of strain S1(T) is only the second genome of a member of the genus Rhodospirillum to be published, but the first type strain genome from the genus. The 4,352,825 bp long chromosome and 53,732 bp plasmid with a total of 3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint Genome Institute Program DOEM 2002.

• Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)).

  Authors: Marcel Huntemann, Megan Lu, Matt Nolan, Alla Lapidus, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia, Cliff Han [......] Stefan Spring, Markus Göker, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, Konstantinos Mavromatis

  Standards in genomic sciences. 07/2011; 4(3):303-11.

  Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderatelyHippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome sequencing because of its isolated phylogenetic location, as a distant next neighbor of the genus Desulfurella. Strain MH(2) (T) is the first type strain from the order Desulfurellales with a completely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein-coding and 57 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Complete genome sequence of the extremely halophilic Halanaerobium praevalens type strain (GSL).

  Authors: Natalia Ivanova, Johannes Sikorski, Olga Chertkov, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia, Cliff Han [......] Markus Göker, John C Detter, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, Alla Lapidus

  Standards in genomic sciences. 07/2011; 4(3):312-21.

  Halanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaerobium, which in turn is the type genus of the family Halanaerobiaceae. The species is of interest because it isHalanaerobium praevalens Zeikus et al. 1984 is the type species of the genus Halanaerobium, which in turn is the type genus of the family Halanaerobiaceae. The species is of interest because it is able to reduce a variety of nitro-substituted aromatic compounds at a high rate, and because of its ability to degrade organic pollutants. The strain is also of interest because it functions as a hydrolytic bacterium, fermenting complex organic matter and producing intermediary metabolites for other trophic groups such as sulfate-reducing and methanogenic bacteria. It is further reported as being involved in carbon removal in the Great Salt Lake, its source of isolation. This is the first completed genome sequence of a representative of the genus Halanaerobium and the second genome sequence from a type strain of the family Halanaerobiaceae. The 2,309,262 bp long genome with its 2,110 protein-coding and 70 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1).

  Authors: Iain Anderson, Johannes Sikorski, Ahmet Zeytun, Matt Nolan, Alla Lapidus, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia [......] Brian J Tindall, Markus Göker, John C Detter, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Hans-Peter Klenk, Nikos C Kyrpides

  Standards in genomic sciences. 07/2011; 4(3):322-30.

  Nitratifractor salsuginis Nakagawa et al. 2005 is the type species of the genus Nitratifractor, a member of the family Nautiliaceae. The species is of interest because of its high capacity forNitratifractor salsuginis Nakagawa et al. 2005 is the type species of the genus Nitratifractor, a member of the family Nautiliaceae. The species is of interest because of its high capacity for nitrate reduction via conversion to N(2) through respiration, which is a key compound in plant nutrition. The strain is also of interest because it represents the first mesophilic and facultatively anaerobic member of the Epsilonproteobacteria reported to grow on molecular hydrogen. This is the first completed genome sequence of a member of the genus Nitratifractor and the second sequence from the family Nautiliaceae. The 2,101,285 bp long genome with its 2,121 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Complete genome sequence of Mahella australiensis type strain (50-1 BON).

  Authors: Johannes Sikorski, Hazuki Teshima, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Sam Pitluck, Konstantinos Liolios, Ioanna Pagani [......] Markus Göker, John C Detter, Tanja Woyke, James Bristow, Victor Markowitz, Philip Hugenholtz, Jonathan A Eisen, Nikos C Kyrpides, Hans-Peter Klenk, Alla Lapidus

  Standards in genomic sciences. 07/2011; 4(3):331-41.

  Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella, which belongs to the family Thermoanaerobacteraceae. The species is of interest because it differs fromMahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella, which belongs to the family Thermoanaerobacteraceae. The species is of interest because it differs from other known anaerobic spore-forming bacteria in its G+C content, and in certain phenotypic traits, such as carbon source utilization and relationship to temperature. Moreover, it has been discussed that this species might be an indigenous member of petroleum and oil reservoirs. This is the first completed genome sequence of a member of the genus Mahella and the ninth completed type strain genome sequence from the family Thermoanaerobacteraceae. The 3,135,972 bp long genome with its 2,974 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Complete genome sequence of Tsukamurella paurometabola type strain (no. 33).

  Authors: A Christine Munk, Alla Lapidus, Susan Lucas, Matt Nolan, Hope Tice, Jan-Fang Cheng, Tijana Glavina Del Rio, Lynne Goodwin, Sam Pitluck, Konstantinos Liolios [......] Johannes Sikorski, Markus Göker, John C Detter, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk

  Standards in genomic sciences. 07/2011; 4(3):342-51.

  Tsukamurella paurometabola corrig. (Steinhaus 1941) Collins et al. 1988 is the type species of the genus Tsukamurella, which is the type genus to the family Tsukamurellaceae. The species is not onlyTsukamurella paurometabola corrig. (Steinhaus 1941) Collins et al. 1988 is the type species of the genus Tsukamurella, which is the type genus to the family Tsukamurellaceae. The species is not only of interest because of its isolated phylogenetic location, but also because it is a human opportunistic pathogen with some strains of the species reported to cause lung infection, lethal meningitis, and necrotizing tenosynovitis. This is the first completed genome sequence of a member of the genus Tsukamurella and the first genome sequence of a member of the family Tsukamurellaceae. The 4,479,724 bp long genome contains a 99,806 bp long plasmid and a total of 4,335 protein-coding and 56 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Complete genome sequence of Haliscomenobacter hydrossis type strain (O).

  Authors: Hajnalka Daligault, Alla Lapidus, Ahmet Zeytun, Matt Nolan, Susan Lucas, Tijana Glavina Del Rio, Hope Tice, Jan-Fang Cheng, Roxanne Tapia, Cliff Han [......] Manfred Rohde, Susanne Verbarg, Markus Göker, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, Tanja Woyke

  Standards in genomic sciences. 07/2011; 4(3):352-60.

  Haliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus Haliscomenobacter, which belongs to order "Sphingobacteriales". The species is of interest because of its isolatedHaliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus Haliscomenobacter, which belongs to order "Sphingobacteriales". The species is of interest because of its isolated phylogenetic location in the tree of life, especially the so far genomically uncharted part of it, and because the organism grows in a thin, hardly visible hyaline sheath. Members of the species were isolated from fresh water of lakes and from ditch water. The genome of H. hydrossis is the first completed genome sequence reported from a member of the family "Saprospiraceae". The 8,771,651 bp long genome with its three plasmids of 92 kbp, 144 kbp and 164 kbp length contains 6,848 protein-coding and 60 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Complete genome sequence of Treponema succinifaciens type strain (6091).

  Authors: Cliff Han, Sabine Gronow, Hazuki Teshima, Alla Lapidus, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Ahmed Zeytun [......] Manfred Rohde, Markus Göker, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, John C Detter

  Standards in genomic sciences. 07/2011; 4(3):361-70.

  Treponema succinifaciens Cwyk and Canale-Parola 1981 is of interest because this strictly anaerobic, apathogenic member of the genus Treponema oxidizes carbohydrates and couples the Embden-MeyerhofTreponema succinifaciens Cwyk and Canale-Parola 1981 is of interest because this strictly anaerobic, apathogenic member of the genus Treponema oxidizes carbohydrates and couples the Embden-Meyerhof pathway via activity of a pyruvate-formate lyase to the production of acetyl-coenzyme A and formate. This feature separates this species from most other anaerobic spirochetes. The genome of T. succinifaciens 6091(T) is only the second completed and published type strain genome from the genus Treponema in the family Spirochaetaceae. The 2,897,425 bp long genome with one plasmid harbors 2,723 protein-coding and 63 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR).

  Authors: Cliff Han, Romano Mwirichia, Olga Chertkov, Brittany Held, Alla Lapidus, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng [......] Johannes Sikorski, Markus Göker, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, John C Detter

  Standards in genomic sciences. 07/2011; 4(3):371-80.

  Syntrophobotulus glycolicus Friedrich et al. 1996 is currently the only member of the genus Syntrophobotulus within the family Peptococcaceae. The species is of interest because of its isolatedSyntrophobotulus glycolicus Friedrich et al. 1996 is currently the only member of the genus Syntrophobotulus within the family Peptococcaceae. The species is of interest because of its isolated phylogenetic location in the genome-sequenced fraction of tree of life. When grown in pure culture with glyoxylate as carbon source the organism utilizes glyoxylate through fermentative oxidation, whereas, when grown in syntrophic co-culture with homoacetogenic or methanogenic bacteria, it is able to oxidize glycolate to carbon dioxide and hydrogen. No other organic or inorganic carbon source is utilized by S. glycolicus. The subdivision of the family Peptococcaceae into genera does not reflect the natural relationships, particularly regarding the genera most closely related to Syntrophobotulus. Both Desulfotomaculum and Pelotomaculum are paraphyletic assemblages, and the taxonomic classification is in significant conflict with the 16S rRNA data. S. glycolicus is already the ninth member of the family Peptococcaceae with a completely sequenced and publicly available genome. The 3,406,739 bp long genome with its 3,370 protein-coding and 69 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A).

  Authors: Iain Anderson, Markus Göker, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia, Cliff Han, Lynne Goodwin [......] Reinhard Wirth, John C Detter, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk, Alla Lapidus

  Standards in genomic sciences. 07/2011; 4(3):381-92.

  Pyrolobus fumarii Blöchl et al. 1997 is the type species of the genus Pyrolobus, which belongs to the crenarchaeal family Pyrodictiaceae. The species is a facultatively microaerophilic non-motilePyrolobus fumarii Blöchl et al. 1997 is the type species of the genus Pyrolobus, which belongs to the crenarchaeal family Pyrodictiaceae. The species is a facultatively microaerophilic non-motile crenarchaeon. It is of interest because of its isolated phylogenetic location in the tree of life and because it is a hyperthermophilic chemolithoautotroph known as the primary producer of organic matter at deep-sea hydrothermal vents. P. fumarii exhibits currently the highest optimal growth temperature of all life forms on earth (106°C). This is the first completed genome sequence of a member of the genus Pyrolobus to be published and only the second genome sequence from a member of the family Pyrodictiaceae. Although Diversa Corporation announced the completion of sequencing of the P. fumarii genome on September 25, 2001, this sequence was never released to the public. The 1,843,267 bp long genome with its 1,986 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

• Complete genome sequence of the acetate-degrading sulfate reducer Desulfobacca acetoxidans type strain (ASRB2).

  Authors: Markus Göker, Hazuki Teshima, Alla Lapidus, Matt Nolan, Susan Lucas, Nancy Hammon, Shweta Deshpande, Jan-Fang Cheng, Roxanne Tapia, Cliff Han [......] Manfred Rohde, Stefan Spring, John C Detter, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk

  Standards in genomic sciences. 07/2011; 4(3):393-401.

  Desulfobacca acetoxidans Elferink et al. 1999 is the type species of the genus Desulfobacca, which belongs to the family Syntrophaceae in the class Deltaproteobacteria. The species was first observedDesulfobacca acetoxidans Elferink et al. 1999 is the type species of the genus Desulfobacca, which belongs to the family Syntrophaceae in the class Deltaproteobacteria. The species was first observed in a study on the competition of sulfate-reducers and acetoclastic methanogens for acetate in sludge. D. acetoxidans is considered to be the most abundant acetate-degrading sulfate reducer in sludge. It is of interest due to its isolated phylogenetic location in the 16S rRNA-based tree of life. This is the second completed genome sequence of a member of the family Syntrophaceae to be published and only the third genome sequence from a member of the order Syntrophobacterales. The 3,282,536 bp long genome with its 2,969 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.