Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T)

Iain Anderson, Brittany Held, Alla Lapidus, Matt Nolan, Susan Lucas, Hope Tice, Tijana Glavina Del Rio, Jan Fang Cheng, Cliff Han, Roxanne Tapia, Lynne A. Good-win, Sam Pitluck, Konstantinos Liolios, Konstantinos Mavromatis, Ioanna Pagani, Natalia Ivanova, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna PalaniappanMiriam Land, Evelyne Marie Brambilla, Manfred Rohde, Stefan Spring, Markus Göker, John C. Detter, Tanja Woyke, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Hans Peter Klenk, Nikos C. Kyrpides

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Holophaga foetida Liesack et al. 1995 is a member of the phylum Acidobacteria and is of in-terest for its ability to anaerobically degrade aromatic compounds and for its production of volatile sulfur compounds through a unique pathway. The genome of H. foetida strain TMBS4T is the first to be sequenced for a representative of the class Holophagae. Here we de-scribe the features of this organism, together with the complete genome sequence (improved high quality draft), and annotation. The 4,127,237 bp long chromosome with its 3,615 pro-tein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Original languageEnglish (US)
Pages (from-to)174-184
Number of pages11
JournalStandards in Genomic Sciences
Volume6
Issue number2
DOIs
StatePublished - 2012

Fingerprint

Acidobacteria
Genome
Encyclopedias
Bacteria
Sulfur Compounds
Archaea
Chromosomes
RNA
Genes

Keywords

  • Acidobacteria
  • Anaerobic
  • Chemoorganotrophic
  • Fresh water mud
  • GEBA
  • Gram-negative
  • Holophagaceae
  • Mesophilic
  • Non-motile
  • Sulfide-methylation

ASJC Scopus subject areas

  • Genetics

Cite this

Anderson, I., Held, B., Lapidus, A., Nolan, M., Lucas, S., Tice, H., ... Kyrpides, N. C. (2012). Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T). Standards in Genomic Sciences, 6(2), 174-184. https://doi.org/10.4056/sigs.2746047

Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T). / Anderson, Iain; Held, Brittany; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Tice, Hope; Del Rio, Tijana Glavina; Cheng, Jan Fang; Han, Cliff; Tapia, Roxanne; Good-win, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Brambilla, Evelyne Marie; Rohde, Manfred; Spring, Stefan; Göker, Markus; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans Peter; Kyrpides, Nikos C.

In: Standards in Genomic Sciences, Vol. 6, No. 2, 2012, p. 174-184.

Research output: Contribution to journalArticle

Anderson, I, Held, B, Lapidus, A, Nolan, M, Lucas, S, Tice, H, Del Rio, TG, Cheng, JF, Han, C, Tapia, R, Good-win, LA, Pitluck, S, Liolios, K, Mavromatis, K, Pagani, I, Ivanova, N, Mikhailova, N, Pati, A, Chen, A, Palaniappan, K, Land, M, Brambilla, EM, Rohde, M, Spring, S, Göker, M, Detter, JC, Woyke, T, Bristow, J, Eisen, JA, Markowitz, V, Hugenholtz, P, Klenk, HP & Kyrpides, NC 2012, 'Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T)', Standards in Genomic Sciences, vol. 6, no. 2, pp. 174-184. https://doi.org/10.4056/sigs.2746047
Anderson, Iain ; Held, Brittany ; Lapidus, Alla ; Nolan, Matt ; Lucas, Susan ; Tice, Hope ; Del Rio, Tijana Glavina ; Cheng, Jan Fang ; Han, Cliff ; Tapia, Roxanne ; Good-win, Lynne A. ; Pitluck, Sam ; Liolios, Konstantinos ; Mavromatis, Konstantinos ; Pagani, Ioanna ; Ivanova, Natalia ; Mikhailova, Natalia ; Pati, Amrita ; Chen, Amy ; Palaniappan, Krishna ; Land, Miriam ; Brambilla, Evelyne Marie ; Rohde, Manfred ; Spring, Stefan ; Göker, Markus ; Detter, John C. ; Woyke, Tanja ; Bristow, James ; Eisen, Jonathan A ; Markowitz, Victor ; Hugenholtz, Philip ; Klenk, Hans Peter ; Kyrpides, Nikos C. / Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T). In: Standards in Genomic Sciences. 2012 ; Vol. 6, No. 2. pp. 174-184.
@article{b5fc1bb172174b0fa8644c925d4ef9e6,
title = "Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T)",
abstract = "Holophaga foetida Liesack et al. 1995 is a member of the phylum Acidobacteria and is of in-terest for its ability to anaerobically degrade aromatic compounds and for its production of volatile sulfur compounds through a unique pathway. The genome of H. foetida strain TMBS4T is the first to be sequenced for a representative of the class Holophagae. Here we de-scribe the features of this organism, together with the complete genome sequence (improved high quality draft), and annotation. The 4,127,237 bp long chromosome with its 3,615 pro-tein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.",
keywords = "Acidobacteria, Anaerobic, Chemoorganotrophic, Fresh water mud, GEBA, Gram-negative, Holophagaceae, Mesophilic, Non-motile, Sulfide-methylation",
author = "Iain Anderson and Brittany Held and Alla Lapidus and Matt Nolan and Susan Lucas and Hope Tice and {Del Rio}, {Tijana Glavina} and Cheng, {Jan Fang} and Cliff Han and Roxanne Tapia and Good-win, {Lynne A.} and Sam Pitluck and Konstantinos Liolios and Konstantinos Mavromatis and Ioanna Pagani and Natalia Ivanova and Natalia Mikhailova and Amrita Pati and Amy Chen and Krishna Palaniappan and Miriam Land and Brambilla, {Evelyne Marie} and Manfred Rohde and Stefan Spring and Markus G{\"o}ker and Detter, {John C.} and Tanja Woyke and James Bristow and Eisen, {Jonathan A} and Victor Markowitz and Philip Hugenholtz and Klenk, {Hans Peter} and Kyrpides, {Nikos C.}",
year = "2012",
doi = "10.4056/sigs.2746047",
language = "English (US)",
volume = "6",
pages = "174--184",
journal = "Environmental Microbiomes",
issn = "1944-3277",
publisher = "BioMed Central Ltd.",
number = "2",

}

TY - JOUR

T1 - Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T)

AU - Anderson, Iain

AU - Held, Brittany

AU - Lapidus, Alla

AU - Nolan, Matt

AU - Lucas, Susan

AU - Tice, Hope

AU - Del Rio, Tijana Glavina

AU - Cheng, Jan Fang

AU - Han, Cliff

AU - Tapia, Roxanne

AU - Good-win, Lynne A.

AU - Pitluck, Sam

AU - Liolios, Konstantinos

AU - Mavromatis, Konstantinos

AU - Pagani, Ioanna

AU - Ivanova, Natalia

AU - Mikhailova, Natalia

AU - Pati, Amrita

AU - Chen, Amy

AU - Palaniappan, Krishna

AU - Land, Miriam

AU - Brambilla, Evelyne Marie

AU - Rohde, Manfred

AU - Spring, Stefan

AU - Göker, Markus

AU - Detter, John C.

AU - Woyke, Tanja

AU - Bristow, James

AU - Eisen, Jonathan A

AU - Markowitz, Victor

AU - Hugenholtz, Philip

AU - Klenk, Hans Peter

AU - Kyrpides, Nikos C.

PY - 2012

Y1 - 2012

N2 - Holophaga foetida Liesack et al. 1995 is a member of the phylum Acidobacteria and is of in-terest for its ability to anaerobically degrade aromatic compounds and for its production of volatile sulfur compounds through a unique pathway. The genome of H. foetida strain TMBS4T is the first to be sequenced for a representative of the class Holophagae. Here we de-scribe the features of this organism, together with the complete genome sequence (improved high quality draft), and annotation. The 4,127,237 bp long chromosome with its 3,615 pro-tein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

AB - Holophaga foetida Liesack et al. 1995 is a member of the phylum Acidobacteria and is of in-terest for its ability to anaerobically degrade aromatic compounds and for its production of volatile sulfur compounds through a unique pathway. The genome of H. foetida strain TMBS4T is the first to be sequenced for a representative of the class Holophagae. Here we de-scribe the features of this organism, together with the complete genome sequence (improved high quality draft), and annotation. The 4,127,237 bp long chromosome with its 3,615 pro-tein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

KW - Acidobacteria

KW - Anaerobic

KW - Chemoorganotrophic

KW - Fresh water mud

KW - GEBA

KW - Gram-negative

KW - Holophagaceae

KW - Mesophilic

KW - Non-motile

KW - Sulfide-methylation

UR - http://www.scopus.com/inward/record.url?scp=84863583206&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84863583206&partnerID=8YFLogxK

U2 - 10.4056/sigs.2746047

DO - 10.4056/sigs.2746047

M3 - Article

C2 - 22768361

AN - SCOPUS:84863583206

VL - 6

SP - 174

EP - 184

JO - Environmental Microbiomes

JF - Environmental Microbiomes

SN - 1944-3277

IS - 2

ER -