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Nature Biotechnology
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The genome sequence of the capnophilic rumen bacteriumMannheimia succiniciproducens

Nature Biotechnologyvolume 22, pages1275–1281 (2004)Cite this article

ACorrigendum to this article was published on 01 December 2004

Abstract

The rumen represents the first section of a ruminant animal's stomach, where feed is collected and mixed with microorganisms for initial digestion. The major gas produced in the rumen is CO2 (65.5 mol%), yet the metabolic characteristics of capnophilic (CO2-loving) microorganisms are not well understood. Here we report the 2,314,078 base pair genome sequence ofMannheimia succiniciproducens MBEL55E, a recently isolated capnophilic Gram-negative bacterium from bovine rumen, and analyze its genome contents and metabolic characteristics. The metabolism ofM. succiniciproducens was found to be well adapted to the oxygen-free rumen by using fumarate as a major electron acceptor. Genome-scale metabolic flux analysis indicated that CO2 is important for the carboxylation of phosphoenolpyruvate to oxaloacetate, which is converted to succinic acid by the reductive tricarboxylic acid cycle and menaquinone systems. This characteristic metabolism allows highly efficient production of succinic acid, an important four-carbon industrial chemical.

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Figure 1: Circular representation of theM. succiniciproducens MBEL55E genome.
Figure 2: Comparison ofM. succiniciproducens MBEL55E ORFs with other organisms.
Figure 3: Results of metabolic flux analyses.
Figure 4: Effects of various metabolic fluxes on the succinic acid fluxes examined by Bayesian network analysis.

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Acknowledgements

We thank Sung Ho Goh and Heyung Ju Shin at the KRIBB, Young Ho Moon, Kang Ryul Choi, Sun Ho Cha, Sung Soo Kim, Soo Hyun Jeong, Eun Mi Chung and Sun Rye Jung at GenoTech, and Jinyoung Park, Sujin Chae and Hee Sun Chung at Bioinfomatix for their contributions during genome sequencing and annotation. This work was supported by the Korean Systems Biology Research Program (M10309020000-03B5002-00000) of the Ministry of Science and Technology (MOST), Bioinfomatix and by the Brain Korea 21 Project. Further support through the LG Chem Chair Professorship and IBM SUR program is appreciated.

Author information

Author notes

  1. Soon Ho Hong and Jin Sik Kim: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Chemical and Biomolecular Engineering, Department of BioSystems, Metabolic and Biomolecular Engineering National Research Laboratory, BioProcess Engineering Research Center and Bioinformatics Research Center, Korea Advanced Institute of Science and Technology, 373–1 Guseong-dong, Yuseong-gu, Daejeon, 305–701, Republic of Korea

    Soon Ho Hong, Jin Sik Kim & Sang Yup Lee

  2. Bioinfomatix, Inc., The fifth floor, Nam Chang Bldg., 748–162 Yeoksam-dong, Gangnam-gu, Seoul, 135–925, Republic of Korea

    Yong Ho In & Sun Shim Choi

  3. Korea Research Institute of Bioscience and Biotechnology (KRIBB), 52 Oun-dong, Yuseong-gu, Daejeon, 305–333, Republic of Korea

    Jeong-Keun Rih, Chang Hoon Kim, Haeyoung Jeong & Cheol Goo Hur

  4. GenoTech Corp., 461–6 Jeonmin-dong, Yuseong-gu, Daejeon, 305–390, Republic of Korea

    Haeyoung Jeong & Jae Jong Kim

  5. IDRTech Inc., 461–6 Jeonmin-dong, Yuseong-gu, Daejeon, 305–390, Republic of Korea

    Yong Ho In

Authors
  1. Soon Ho Hong
  2. Jin Sik Kim
  3. Sang Yup Lee
  4. Yong Ho In
  5. Sun Shim Choi
  6. Jeong-Keun Rih
  7. Chang Hoon Kim
  8. Haeyoung Jeong
  9. Cheol Goo Hur
  10. Jae Jong Kim

Corresponding author

Correspondence toSang Yup Lee.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Fig. 1

M. succiniciproducens MBEL55E genome characteristics. (PDF 956 kb)

Supplementary Fig. 2

A schematic diagram of the entire metabolic network. (PDF 170 kb)

Supplementary Fig. 3

Comparative analysis of the respiratory systems in various microorganisms. (PDF 150 kb)

Supplementary Fig. 4

Time profiles of batch fermentation under various conditions. (PDF 38 kb)

Supplementary Table 1

List ofM. succiniciproducens MBEL55E genes. (PDF 214 kb)

Supplementary Table 2

Functional analysis ofM. succiniciproducens MBEL55E genome. (PDF 52 kb)

Supplementary Table 3

Thein silico metabolic network. (PDF 98 kb)

Supplementary Table 4

Utilization of various carbon sources. (PDF 21 kb)

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Hong, S., Kim, J., Lee, S.et al. The genome sequence of the capnophilic rumen bacteriumMannheimia succiniciproducens.Nat Biotechnol22, 1275–1281 (2004). https://doi.org/10.1038/nbt1010

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