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

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

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

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 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.

Original languageEnglish (US)
Pages (from-to)371-380
Number of pages10
JournalStandards in Genomic Sciences
Volume4
Issue number3
DOIs
StatePublished - 2011

Fingerprint

Peptococcaceae
glycolic acid
Genome
Desulfotomaculum
Carbon
Encyclopedias
Bacteria
Archaea
Coculture Techniques
Carbon Dioxide
Hydrogen
RNA
Genes
Proteins
glyoxylic acid

Keywords

  • Chemotrophic
  • Clostridiales
  • GEBA
  • Glycolate-oxidizing
  • Gram-negative with gram-positive cell wall structure
  • Mesophilic
  • Non-motile
  • Peptococca-ceae
  • Rod-shaped
  • Spore-forming
  • Strictly anaerobic

ASJC Scopus subject areas

  • Genetics

Cite this

Han, C., Mwirichia, R., Chertkov, O., Held, B., Lapidus, A., Nolan, M., ... Detter, J. C. (2011). Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR T). Standards in Genomic Sciences, 4(3), 371-380. https://doi.org/10.4056/sigs.2004648

Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR T). / Han, Cliff; Mwirichia, Romano; Chertkov, Olga; Held, Brittany; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan Fang; Tapia, Roxanne; Goodwin, Lynne; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Ivanova, Natalia; Pagani, Ioanna; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Brambilla, Evelyne Marie; Rohde, Manfred; Spring, Stefan; Sikorski, Johannes; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans Peter; Detter, John C.

In: Standards in Genomic Sciences, Vol. 4, No. 3, 2011, p. 371-380.

Research output: Contribution to journalArticle

Han, C, Mwirichia, R, Chertkov, O, Held, B, Lapidus, A, Nolan, M, Lucas, S, Hammon, N, Deshpande, S, Cheng, JF, Tapia, R, Goodwin, L, Pitluck, S, Huntemann, M, Liolios, K, Ivanova, N, Pagani, I, Mavromatis, K, Ovchinikova, G, Pati, A, Chen, A, Palaniappan, K, Land, M, Hauser, L, Brambilla, EM, Rohde, M, Spring, S, Sikorski, J, Göker, M, Woyke, T, Bristow, J, Eisen, JA, Markowitz, V, Hugenholtz, P, Kyrpides, NC, Klenk, HP & Detter, JC 2011, 'Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR T)', Standards in Genomic Sciences, vol. 4, no. 3, pp. 371-380. https://doi.org/10.4056/sigs.2004648
Han, Cliff ; Mwirichia, Romano ; Chertkov, Olga ; Held, Brittany ; Lapidus, Alla ; Nolan, Matt ; Lucas, Susan ; Hammon, Nancy ; Deshpande, Shweta ; Cheng, Jan Fang ; Tapia, Roxanne ; Goodwin, Lynne ; Pitluck, Sam ; Huntemann, Marcel ; Liolios, Konstantinos ; Ivanova, Natalia ; Pagani, Ioanna ; Mavromatis, Konstantinos ; Ovchinikova, Galina ; Pati, Amrita ; Chen, Amy ; Palaniappan, Krishna ; Land, Miriam ; Hauser, Loren ; Brambilla, Evelyne Marie ; Rohde, Manfred ; Spring, Stefan ; Sikorski, Johannes ; Göker, Markus ; Woyke, Tanja ; Bristow, James ; Eisen, Jonathan A ; Markowitz, Victor ; Hugenholtz, Philip ; Kyrpides, Nikos C. ; Klenk, Hans Peter ; Detter, John C. / Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR T). In: Standards in Genomic Sciences. 2011 ; Vol. 4, No. 3. pp. 371-380.
@article{40e6b2efaab74ce7aae733c25f3c476a,
title = "Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR T)",
abstract = "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 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.",
keywords = "Chemotrophic, Clostridiales, GEBA, Glycolate-oxidizing, Gram-negative with gram-positive cell wall structure, Mesophilic, Non-motile, Peptococca-ceae, Rod-shaped, Spore-forming, Strictly anaerobic",
author = "Cliff Han and Romano Mwirichia and Olga Chertkov and Brittany Held and Alla Lapidus and Matt Nolan and Susan Lucas and Nancy Hammon and Shweta Deshpande and Cheng, {Jan Fang} and Roxanne Tapia and Lynne Goodwin and Sam Pitluck and Marcel Huntemann and Konstantinos Liolios and Natalia Ivanova and Ioanna Pagani and Konstantinos Mavromatis and Galina Ovchinikova and Amrita Pati and Amy Chen and Krishna Palaniappan and Miriam Land and Loren Hauser and Brambilla, {Evelyne Marie} and Manfred Rohde and Stefan Spring and Johannes Sikorski and Markus G{\"o}ker and Tanja Woyke and James Bristow and Eisen, {Jonathan A} and Victor Markowitz and Philip Hugenholtz and Kyrpides, {Nikos C.} and Klenk, {Hans Peter} and Detter, {John C.}",
year = "2011",
doi = "10.4056/sigs.2004648",
language = "English (US)",
volume = "4",
pages = "371--380",
journal = "Environmental Microbiomes",
issn = "1944-3277",
publisher = "BioMed Central Ltd.",
number = "3",

}

TY - JOUR

T1 - Complete genome sequence of Syntrophobotulus glycolicus type strain (FlGlyR T)

AU - Han, Cliff

AU - Mwirichia, Romano

AU - Chertkov, Olga

AU - Held, Brittany

AU - Lapidus, Alla

AU - Nolan, Matt

AU - Lucas, Susan

AU - Hammon, Nancy

AU - Deshpande, Shweta

AU - Cheng, Jan Fang

AU - Tapia, Roxanne

AU - Goodwin, Lynne

AU - Pitluck, Sam

AU - Huntemann, Marcel

AU - Liolios, Konstantinos

AU - Ivanova, Natalia

AU - Pagani, Ioanna

AU - Mavromatis, Konstantinos

AU - Ovchinikova, Galina

AU - Pati, Amrita

AU - Chen, Amy

AU - Palaniappan, Krishna

AU - Land, Miriam

AU - Hauser, Loren

AU - Brambilla, Evelyne Marie

AU - Rohde, Manfred

AU - Spring, Stefan

AU - Sikorski, Johannes

AU - Göker, Markus

AU - Woyke, Tanja

AU - Bristow, James

AU - Eisen, Jonathan A

AU - Markowitz, Victor

AU - Hugenholtz, Philip

AU - Kyrpides, Nikos C.

AU - Klenk, Hans Peter

AU - Detter, John C.

PY - 2011

Y1 - 2011

N2 - 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 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.

AB - 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 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.

KW - Chemotrophic

KW - Clostridiales

KW - GEBA

KW - Glycolate-oxidizing

KW - Gram-negative with gram-positive cell wall structure

KW - Mesophilic

KW - Non-motile

KW - Peptococca-ceae

KW - Rod-shaped

KW - Spore-forming

KW - Strictly anaerobic

UR - http://www.scopus.com/inward/record.url?scp=80053371757&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80053371757&partnerID=8YFLogxK

U2 - 10.4056/sigs.2004648

DO - 10.4056/sigs.2004648

M3 - Article

AN - SCOPUS:80053371757

VL - 4

SP - 371

EP - 380

JO - Environmental Microbiomes

JF - Environmental Microbiomes

SN - 1944-3277

IS - 3

ER -