Understanding a Methanogenic Benzene-degrading Culture using Metabolic Models Created from Metagenomic Sequences

• Main Author: Ho, Hanchen
• Other Authors: Mahadevan, Radhakrishnan
• Language: en_ca
• Published: 2013
• Subjects: modeling; metagenomics; 0542
• Online Access: http://hdl.handle.net/1807/42861

Metabolic models were constructed from the metagenome of a methanogenic benzene-degrading community to understand the metabolite interactions among the key microbes in the culture. The metagenomic sequences were assembled, and it was found that assembling the short DNA fragments before they were combined with longer reads can contribute to the overall lengths of the resulting sequences. The metagenome was then taxonomically classified into the domain of archaea and bacteria, and domain-specific models were built. A mathematical framework to fill metabolic gaps at the community level was then developed and applied to the benzene-degrading community model to study how metabolic gaps can be filled by via interspecies metabolite transfer, and it suggested that among other metabolites, acetate, hydrogen, formate, coenzyme A and histidine produced by the bacteria population could potentially contribute to the growth of the methanogens. The computational framework demonstrated its ability to generate testable hypotheses about microbial interactions.