Microbial fuel cells are bioenergy sources in which electricity is produced through anaerobic catalysis of organic matter using a biocatalyst. The current limitation of these systems is low power production that prevents them from being used as a viable source of energy. One of the most comprehensive solutions to overcome this limitation is genetic modification to enhance the extracellular electron transport in exoelectrogene bacteria such as Shewanella oneidensis MR-1. To embark on this modification, the genes involved in extracellular electron transport and their interactions need to be well understood in advance. One technique to identify those genes expressed in extracellular electron transport is their differential expression under perturbed environmental conditions. Barchinger et al. (2016) applied oxygen limitation to a Shewanella oneidensis MR-1chemostat culture and produced RNA-Seq data to obtain 50-bp single-end reads for the collected samples. The sequence data have been deposited in the Gene Expression Omnibus database under accession number GSE79964. In this work, using two gene expression data analysis softwares, SPARTA and Rockhopper, the RNA-Seq data was analyzed. In this analysis, the regulation of differentially expressed genes under oxygen limitation was investigated and the most regulated gene cluster in shifting from aerobic to anaerobic extracellular electron transport were identified.

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