Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT)

Han, Cliff; Mwirichia, Romano; Chertkov, Olga; Held, Brittany; Lapidus, Alla L; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Ivanova, N; Pagani, Ioanna; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Sikorski, Johannes; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Detter, J Chris

doi:10.4056/sigs.2004648

Title: Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT)

Journal Article · Sat Jan 01 00:00:00 EST 2011 · Standards in Genomic Sciences

DOI:https://doi.org/10.4056/sigs.2004648· OSTI ID:1049904

Han, Cliff ^[1]; Mwirichia, Romano ^[2]; Chertkov, Olga ^[1]; Held, Brittany ^[1]; Lapidus, Alla L ^[3]; Nolan, Matt ^[3]; Lucas, Susan ^[3]; Hammon, Nancy ^[3]; Deshpande, Shweta ^[3]; Cheng, Jan-Fang ^[3]; Tapia, Roxanne ^[1]; Goodwin, Lynne A ^[1]; Pitluck, Sam ^[3]; Huntemann, Marcel ^[3]; Liolios, Konstantinos ^[3]; Ivanova, N ^[3]; Pagani, Ioanna ^[3]; Mavromatis, K ^[3]; Ovchinnikova, Galina ^[3]; Pati, Amrita ^[3] more »

Los Alamos National Laboratory (LANL)
Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
U.S. Department of Energy, Joint Genome Institute
ORNL
DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany

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 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 re- garding the genera most closely related to Syntrophobotulus. Both Desulfotomaculum and Pelotomaculum are paraphyletic assemblages, and the taxonomic classification is in signifi- cant 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.

Cite

Export

Save

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: Work for Others (WFO)

DOE Contract Number:: AC05-00OR22725

OSTI ID:: 1049904

Journal Information:: Standards in Genomic Sciences, Vol. 4, Issue 3; ISSN 1944-3277

Publisher:: BioMed Central

Country of Publication:: United States

Language:: English

References (32)

List of Bacterial Names with Standing in Nomenclature: a Folder Available on the Internet EuzéBy, J. P. International Journal of Systematic and Evolutionary Microbiology, Vol. 47, Issue 2 https://doi.org/10.1099/00207713-47-2-590	journal	April 1997
Phylogenetic Positions of Desulfofustis glycolicus gen. nov., sp. nov. and Syntrophobotulus glycolicus gen. nov., sp. nov., Two New Strict Anaerobes Growing with Glycolic Acid Friedrich, M.; Springer, N.; Ludwig, W. International Journal of Systematic Bacteriology, Vol. 46, Issue 4 https://doi.org/10.1099/00207713-46-4-1065	journal	October 1996
The production of glycollate during photosynthesis in Chlorella Whittingham, C. P.; Pritchard, G. G. Proceedings of the Royal Society of London. Series B. Biological Sciences, Vol. 157, Issue 968, p. 366-382 https://doi.org/10.1098/rspb.1963.0017	journal	March 1963
Glycollate formation and excretion by the purple photosynthetic bacterium Rhodospirillum rubrum Codd, G. A.; Smith, B. M. FEBS Letters, Vol. 48, Issue 1 https://doi.org/10.1016/0014-5793(74)81073-2	journal	November 1974
Glycollate production and excretion byAlcaligenes eutrophus Codd, G. A.; Bowien, B.; Schlegel, H. G. Archives of Microbiology, Vol. 110, Issue 2-3 https://doi.org/10.1007/BF00690224	journal	November 1976
Fermentative degradation of glycolic acid by defined syntrophic cocultures Friedrich, Michael; Laderer, Ute; Schink, Bernhard Archives of Microbiology, Vol. 156, Issue 5 https://doi.org/10.1007/BF00248717	journal	October 1991
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
An algorithm for suffix stripping Porter, M. F. Program, Vol. 14, Issue 3 https://doi.org/10.1108/eb046814	journal	March 1980
Microbial structure of an anaerobic bioreactor population that continuously dechlorinates 1,2-dichloropropane Schlötelburg, C. FEMS Microbiology Ecology, Vol. 39, Issue 3 https://doi.org/10.1016/S0168-6496(02)00177-0	journal	March 2002
Multiple sequence alignment using partial order graphs Lee, C.; Grasso, C.; Sharlow, M. F. Bioinformatics, Vol. 18, Issue 3 https://doi.org/10.1093/bioinformatics/18.3.452	journal	March 2002
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis Castresana, J. Molecular Biology and Evolution, Vol. 17, Issue 4 https://doi.org/10.1093/oxfordjournals.molbev.a026334	journal	April 2000
A Rapid Bootstrap Algorithm for the RAxML Web Servers Stamatakis, Alexandros; Hoover, Paul; Rougemont, Jacques Systematic Biology, Vol. 57, Issue 5 https://doi.org/10.1080/10635150802429642	journal	October 2008
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp848	journal	November 2009
Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T) Spring, Stefan; Lapidus, Alla; Schröder, Maren Standards in Genomic Sciences, Vol. 1, Issue 3 https://doi.org/10.4056/sigs.39508	journal	November 2009
The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota Kosaka, T.; Kato, S.; Shimoyama, T. Genome Research, Vol. 18, Issue 3 https://doi.org/10.1101/gr.7136508	journal	February 2008
Complete Genome Sequence of the Dehalorespiring Bacterium Desulfitobacterium hafniense Y51 and Comparison with Dehalococcoides ethenogenes 195 Nonaka, H.; Keresztes, G.; Shinoda, Y. Journal of Bacteriology, Vol. 188, Issue 6 https://doi.org/10.1128/JB.188.6.2262-2274.2006	journal	March 2006
The minimum information about a genome sequence (MIGS) specification Field, Dawn; Garrity, George; Gray, Tanya Nature Biotechnology, Vol. 26, Issue 5 https://doi.org/10.1038/nbt1360	journal	May 2008
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Woese, C. R.; Kandler, O.; Wheelis, M. L. Proceedings of the National Academy of Sciences, Vol. 87, Issue 12 https://doi.org/10.1073/pnas.87.12.4576	journal	June 1990
Proposals Concerning the Higher Taxa of Bacteria Gibbons, N. E.; Murray, R. G. E. International Journal of Systematic Bacteriology, Vol. 28, Issue 1 https://doi.org/10.1099/00207713-28-1-1	journal	January 1978
Approved Lists of Bacterial Names Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D. International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1 https://doi.org/10.1099/00207713-30-1-225	journal	January 1980
Peptococcaceae, a New Family To Include the Gram-Positive, Anaerobic Cocci of the Genera Peptococcus, Peptostreptococcus, and Ruminococcus Rogosa, M. International Journal of Systematic Bacteriology, Vol. 21, Issue 3 https://doi.org/10.1099/00207713-21-3-234	journal	July 1971
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
Hydrogen formation from glycolate driven by reversed electron transport in membrane vesicles of a syntrophic glycolate-oxidizing bacterium Friedrich, Michael; Schink, Bernhard European Journal of Biochemistry, Vol. 217, Issue 1 https://doi.org/10.1111/j.1432-1033.1993.tb18238.x	journal	October 1993
Electron transport phosphorylation driven by glyoxylate respiration with hydrogen as electron donor in membrane vesicles of a glyoxylate-fermenting bacterium Friedrich, Michael; Schink, Bernhard Archives of Microbiology, Vol. 163, Issue 4 https://doi.org/10.1007/BF00393379	journal	April 1995
En route to a genome-based classification of Archaea and Bacteria? Klenk, H. -P.; Göker, M. Systematic and Applied Microbiology, Vol. 33, Issue 4 https://doi.org/10.1016/j.syapm.2010.03.003	journal	June 2010
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos Nature, Vol. 462, Issue 7276 https://doi.org/10.1038/nature08656	journal	December 2009
The DNA Bank Network: The Start from a German Initiative Gemeinholzer, Birgit; Dröge, Gabriele; Zetzsche, Holger Biopreservation and Biobanking, Vol. 9, Issue 1 https://doi.org/10.1089/bio.2010.0029	journal	March 2011
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
Complete genome sequence of Kytococcus sedentarius type strain (541T) Sims, David; Brettin, Thomas; Detter, John C. Standards in Genomic Sciences, Vol. 1, Issue 1 https://doi.org/10.4056/sigs.761	journal	July 2009
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia Nature Methods, Vol. 7, Issue 6 https://doi.org/10.1038/nmeth.1457	journal	May 2010
IMG ER: a system for microbial genome annotation expert review and curation Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N. Bioinformatics, Vol. 25, Issue 17 https://doi.org/10.1093/bioinformatics/btp393	journal	June 2009

Similar Records

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

Journal Article · Fri Jul 01 00:00:00 EDT 2011 · Standards in Genomic Sciences · OSTI ID:1049904

Han, Cliff; Mwirichia, Romano; Chertkov, Olga; +34 more

Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305^T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

Journal Article · Mon Dec 08 00:00:00 EST 2014 · Standards in Genomic Sciences · OSTI ID:1049904

Scheuner, Carmen; Tindall, Brian J.; Lu, Megan; +27 more

‘ Candidatus Dichloromethanomonas elyunquensis’ gen. nov., sp. nov., a dichloromethane-degrading anaerobe of the Peptococcaceae family

Journal Article · Wed Dec 21 00:00:00 EST 2016 · Systematic and Applied Microbiology · OSTI ID:1049904

Kleindienst, Sara; Higgins, Steven A.; Tsementzi, Despina; +4 more

Related Subjects

08 HYDROGEN
BACTERIA
CARBON DIOXIDE
CARBON SOURCES
CLASSIFICATION
GENES
HYDROGEN
METHANOGENIC BACTERIA
OXIDATION
RNA
STRAINS
glycolate-oxidizing
Gram-negative with Gram-positive cell wall structure
strictly anaerobic
chemotrophic
mesophilic
non-motile
rod-shaped
spore-forming
Peptococca- ceae
Clostridiales
GEBA

Title: Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyRT)

Citation Formats

References (32)

Similar Records

Related Subjects