Analysis of Metabolic Functionality and Thermodynamic Feasibility of a Metagenomic Sample from “El Coquito” Hot Spring
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.
KeywordsMetabolic reconstruction Thermodynamic restrictions Network topology
Unable to display preview. Download preview PDF.
- 2.Jeffries, T.C., Seymour, J.R., Gilbert, J.A., Dinsdale, E.A., Newton, K., Leterme, S.S.C., Roudnew, B., Smith, R.J., Seuront, L., Mitchell, J.G.: Substrate Type Determines Metagenomic Profiles from Diverse Chemical Habitats. PLoS ONE 6, e25173 (2011)Google Scholar
- 4.Dinsdale, E.A., Edwards, R.A., Hall, D., Angly, F., Breitbart, M., Brulc, J.M., Furlan, M., Desnues, C., Haynes, M., Li, L.L., McDaniel, L., Moran, M.A., Nelson, K.E., Nilsson, C., Olson, R., Paul, J., Brito, B.R., Ruan, Y.J., Swan, B.K., Stevens, R., Valentine, D.L., Thurber, R.V., Wegley, L., White, B.A., Rohwer, F.: Functional metagenomic profiling of nine biomes. Nature 452 (2008)Google Scholar
- 5.Logares, R., Haverkamp, T.H.A., Kumar, S., Lanzén, A., Nederbragt, A.J., Quince, C., Kauserud, H.: Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches. Journal of Microbiological Methods 91, 106–113 (2012)CrossRefGoogle Scholar
- 7.Lewin, A., Wentzel, A., Valla, S.: Metagenomics of microbial life in extreme temperature environments. Current Opinion in BiotechnologyGoogle Scholar
- 8.Jones, D.S., Albrecht, H.L., Dawson, K.S., Schaperdoth, I., Freeman, K.H., Pi, Y., Pearson, A., Macalady, J.L.: Community genomic analysis of an extremely acidophilic sulfur-oxidizing biofilm. ISME 6 (2012)Google Scholar
- 10.Mavrovounotis, M.: Estimation of standard Gibbs energy changes of biotransformations. The Journal of Biological Chemistry 266, 14440–14445 (1991)Google Scholar
- 13.Bohorquez, L.C., Delgado-Serrano, L., López, G., Osorio-Forero, C., Klepac-Ceraj, V., Kolter, R., Junca, H., Baena, S., Zambrano, M.M.: In-depth characterization via complementing culture-independent approaches of the microbial community in an acidic hot spring of the Colombian Andes. Microb. Ecol. 63, 103–115 (2012)CrossRefGoogle Scholar