Complete genome sequence of acidaminococcus fermentans type strain (VR4 T)

Yun Juan Chang; Rüdiger Pukall; Elizabeth Saunders; Alla Lapidus; Alex Copeland; Matt Nolan; Tijana Glavina del Rio; Susan Lucas; Feng Chen; Hope Tice; Jan Fang Cheng; Cliff Han; John C. Detter; David Bruce; Lynne Goodwin; Sam Pitluck; Natalia Mikhailova; Konstantinos Liolios; Amrita Pati; Natalia Ivanova; Konstantinos Mavromatis; Amy Chen; Krishna Palaniappan; Miriam Land; Loren Hauser; Cynthia D. Jeffries; Thomas Brettin; Manfred Rohde; Markus Göker; James Bristow; Jonathan A Eisen; Victor Markowitz; Philip Hugenholtz; Nikos C. Kyrpides; Hans Peter Klenk

doi:10.4056/sigs.1002553

Complete genome sequence of acidaminococcus fermentans type strain (VR4 ^T)

Yun Juan Chang, Rüdiger Pukall, Elizabeth Saunders, Alla Lapidus, Alex Copeland, Matt Nolan, Tijana Glavina del Rio, Susan Lucas, Feng Chen, Hope Tice, Jan Fang Cheng, Cliff Han, John C. Detter, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Mikhailova, Konstantinos Liolios, Amrita Pati, Natalia IvanovaKonstantinos Mavromatis, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Cynthia D. Jeffries, Thomas Brettin, Manfred Rohde, Markus Göker, James Bristow, Jonathan A Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans Peter Klenk

Medical Microbiology and Immunology

Research output: Contribution to journal › Article › peer-review

17 Scopus citations

Abstract

Acidaminococcus fermentans (Rogosa 1969) is the type species of the genus Acidaminococ-cus, and is of phylogenetic interest because of its isolated placement in a genomically little characterized region of the Firmicutes. A. fermentans is known for its habitation of the ga-strointestinal tract and its ability to oxidize trans-aconitate. Its anaerobic fermentation of glu-tamate has been intensively studied and will now be complemented by the genomic basis. The strain described in this report is a nonsporulating, nonmotile, Gram-negative coccus, originally isolated from a pig alimentary tract. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete ge-nome sequence of a member of the family Acidaminococcaceae, and the 2,329,769 bp long genome with its 2,101 protein-coding and 81 RNA genes is part of the Genomic Encyclope-dia of Bacteria and Archaea project.

Original language	English (US)
Pages (from-to)	1-14
Number of pages	14
Journal	Standards in Genomic Sciences
Volume	3
Issue number	1
DOIs	https://doi.org/10.4056/sigs.1002553
State	Published - 2010

Keywords

Acidaminococcaceae
Anaerobic
Diplococcus
Gastrointestinal tract
GEBA
Glutamate fermentation
Mesophile
Negativicutes
Selenomonadales
Trans-aconitate degrada-tion

ASJC Scopus subject areas

Genetics

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10.4056/sigs.1002553

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Chang, Y. J., Pukall, R., Saunders, E., Lapidus, A., Copeland, A., Nolan, M., del Rio, T. G., Lucas, S., Chen, F., Tice, H., Cheng, J. F., Han, C., Detter, J. C., Bruce, D., Goodwin, L., Pitluck, S., Mikhailova, N., Liolios, K., Pati, A., ... Klenk, H. P. (2010). Complete genome sequence of acidaminococcus fermentans type strain (VR4 ^T). Standards in Genomic Sciences, 3(1), 1-14. https://doi.org/10.4056/sigs.1002553

Complete genome sequence of acidaminococcus fermentans type strain (VR4 ^T). / Chang, Yun Juan; Pukall, Rüdiger; Saunders, Elizabeth; Lapidus, Alla; Copeland, Alex; Nolan, Matt; del Rio, Tijana Glavina; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan Fang; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mikhailova, Natalia; Liolios, Konstantinos; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D.; Brettin, Thomas; Rohde, Manfred; Göker, Markus; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans Peter.

In: Standards in Genomic Sciences, Vol. 3, No. 1, 2010, p. 1-14.

Research output: Contribution to journal › Article › peer-review

Chang, YJ, Pukall, R, Saunders, E, Lapidus, A, Copeland, A, Nolan, M, del Rio, TG, Lucas, S, Chen, F, Tice, H, Cheng, JF, Han, C, Detter, JC, Bruce, D, Goodwin, L, Pitluck, S, Mikhailova, N, Liolios, K, Pati, A, Ivanova, N, Mavromatis, K, Chen, A, Palaniappan, K, Land, M, Hauser, L, Jeffries, CD, Brettin, T, Rohde, M, Göker, M, Bristow, J, Eisen, JA, Markowitz, V, Hugenholtz, P, Kyrpides, NC & Klenk, HP 2010, 'Complete genome sequence of acidaminococcus fermentans type strain (VR4 ^T)', Standards in Genomic Sciences, vol. 3, no. 1, pp. 1-14. https://doi.org/10.4056/sigs.1002553

Chang, Yun Juan ; Pukall, Rüdiger ; Saunders, Elizabeth ; Lapidus, Alla ; Copeland, Alex ; Nolan, Matt ; del Rio, Tijana Glavina ; Lucas, Susan ; Chen, Feng ; Tice, Hope ; Cheng, Jan Fang ; Han, Cliff ; Detter, John C. ; Bruce, David ; Goodwin, Lynne ; Pitluck, Sam ; Mikhailova, Natalia ; Liolios, Konstantinos ; Pati, Amrita ; Ivanova, Natalia ; Mavromatis, Konstantinos ; Chen, Amy ; Palaniappan, Krishna ; Land, Miriam ; Hauser, Loren ; Jeffries, Cynthia D. ; Brettin, Thomas ; Rohde, Manfred ; Göker, Markus ; Bristow, James ; Eisen, Jonathan A ; Markowitz, Victor ; Hugenholtz, Philip ; Kyrpides, Nikos C. ; Klenk, Hans Peter. / Complete genome sequence of acidaminococcus fermentans type strain (VR4 ^T). In: Standards in Genomic Sciences. 2010 ; Vol. 3, No. 1. pp. 1-14.

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abstract = "Acidaminococcus fermentans (Rogosa 1969) is the type species of the genus Acidaminococ-cus, and is of phylogenetic interest because of its isolated placement in a genomically little characterized region of the Firmicutes. A. fermentans is known for its habitation of the ga-strointestinal tract and its ability to oxidize trans-aconitate. Its anaerobic fermentation of glu-tamate has been intensively studied and will now be complemented by the genomic basis. The strain described in this report is a nonsporulating, nonmotile, Gram-negative coccus, originally isolated from a pig alimentary tract. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete ge-nome sequence of a member of the family Acidaminococcaceae, and the 2,329,769 bp long genome with its 2,101 protein-coding and 81 RNA genes is part of the Genomic Encyclope-dia of Bacteria and Archaea project.",

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AU - Saunders, Elizabeth

AU - Lapidus, Alla

AU - Copeland, Alex

AU - Nolan, Matt

AU - del Rio, Tijana Glavina

AU - Lucas, Susan

AU - Chen, Feng

AU - Tice, Hope

AU - Cheng, Jan Fang

AU - Han, Cliff

AU - Detter, John C.

AU - Bruce, David

AU - Goodwin, Lynne

AU - Pitluck, Sam

AU - Mikhailova, Natalia

AU - Liolios, Konstantinos

AU - Pati, Amrita

AU - Ivanova, Natalia

AU - Mavromatis, Konstantinos

AU - Chen, Amy

AU - Palaniappan, Krishna

AU - Land, Miriam

AU - Hauser, Loren

AU - Jeffries, Cynthia D.

AU - Brettin, Thomas

AU - Rohde, Manfred

AU - Göker, Markus

AU - Bristow, James

AU - Eisen, Jonathan A

AU - Markowitz, Victor

AU - Hugenholtz, Philip

AU - Kyrpides, Nikos C.

AU - Klenk, Hans Peter

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