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Advances in Computational Biology pp 287–293Cite as

Analysis of Metabolic Functionality and Thermodynamic Feasibility of a Metagenomic Sample from “El Coquito” Hot Spring

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Part of the Advances in Intelligent Systems and Computing book series (AISC,volume 232)

Abstract

The study of metagenomic samples is crucial for understanding microbial communities. In this study, genomic samples of the “El Coquito” hot spring were analysed to identify their metabolic functionality, the thermodynamic restrictions and the influence of biogeochemical cycles. The metabolic functionality was determined assigning reactions and enzymes to the metabolic routes. To determinate the reversibility of the reactions we used the group contribution method. We also performed a topological analysis of the network. We found a total amount of 1930 reactions and 130 metabolic pathways. It was determined that at a pH of 3 there was 256 irreversible reactions and that the reactions involved in energy metabolism belonged to Carbon Fixation, Nitrogen and ammonia assimilation, and sulphur reduction. We found that the “El Coquito” metabolic network is a free scale network and that the clustering coefficients vary if the thermodynamic restrictions are included.

Keywords

  • Metabolic reconstruction
  • Thermodynamic restrictions
  • Network topology

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  • DOI: 10.1007/978-3-319-01568-2_41
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Author information

Authors and Affiliations

  1. Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería química, Universidad de los Andes, Bogotá, Colombia

    Maria A. Zamora & Andrés Fernando González Barrios

  2. Centro de Bioinformática y Biología Computacional, Manizales, Colombia

    Andres Pinzón

  3. GEBIX- Centro Colombiano de Genómica y Bioinformática, Bogotá, Colombia

    Maria M. Zambrano

  4. Laboratorio de Micología y Fitopatología, Departamento de Ciencias biológicas, Universidad de los Andes, Bogotá, Colombia

    Silvia Restrepo

  5. Departament of Chemical and Biological Engineering, McCormick School of Engineering, and Applied Sciences, Northwestern University, Evanston, Illinois, USA

    Linda J. Broadbelt & Matthew Moura

Authors
  1. Maria A. Zamora
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  2. Andres Pinzón
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  3. Maria M. Zambrano
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  4. Silvia Restrepo
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  5. Linda J. Broadbelt
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  6. Matthew Moura
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  7. Andrés Fernando González Barrios
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Corresponding author

Correspondence to Maria A. Zamora .

Editor information

Editors and Affiliations

  1. University of Caldas, Manizales, Colombia

    Luis F. Castillo

  2. Cenicafé - Centro Nacional de Investigaciones del Café en Colombia, Chinchiná, Colombia

    Marco Cristancho

  3. University of Caldas, Manizales, Colombia

    Gustavo Isaza

  4. BIOS - Centro Bioinformática y Biologia Computacional de Colombia, Manizales, Colombia

    Andrés Pinzón

  5. Department of Computer Science School of Science, University of Salamanca, Salamanca, Spain

    Juan Manuel Corchado Rodríguez

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Zamora, M.A. et al. (2014). Analysis of Metabolic Functionality and Thermodynamic Feasibility of a Metagenomic Sample from “El Coquito” Hot Spring. In: Castillo, L., Cristancho, M., Isaza, G., Pinzón, A., Rodríguez, J. (eds) Advances in Computational Biology. Advances in Intelligent Systems and Computing, vol 232. Springer, Cham. https://doi.org/10.1007/978-3-319-01568-2_41

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  • DOI: https://doi.org/10.1007/978-3-319-01568-2_41

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-01567-5

  • Online ISBN: 978-3-319-01568-2

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