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

  • Maria A. Zamora
  • Andres Pinzón
  • Maria M. Zambrano
  • Silvia Restrepo
  • Linda J. Broadbelt
  • Matthew Moura
  • Andrés Fernando González Barrios
Conference paper

DOI: 10.1007/978-3-319-01568-2_41

Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 232)
Cite this paper as:
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

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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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Maria A. Zamora
    • 1
  • Andres Pinzón
    • 2
  • Maria M. Zambrano
    • 3
  • Silvia Restrepo
    • 4
  • Linda J. Broadbelt
    • 5
  • Matthew Moura
    • 5
  • Andrés Fernando González Barrios
    • 1
  1. 1.Grupo de Diseño de Productos y Procesos (GDPP), Departamento de Ingeniería químicaUniversidad de los AndesBogotáColombia
  2. 2.Centro de Bioinformática y Biología ComputacionalManizalesColombia
  3. 3.GEBIX- Centro Colombiano de Genómica y BioinformáticaBogotáColombia
  4. 4.Laboratorio de Micología y Fitopatología, Departamento de Ciencias biológicasUniversidad de los AndesBogotáColombia
  5. 5.Departament of Chemical and Biological Engineering, McCormick School of Engineering, and Applied SciencesNorthwestern UniversityEvanstonUSA

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