The GO Ontology analysis that was inclusive of biological processes, molecular functions and cellular components, was used to classify the functions of the DEGs between WT and ΔnirS. Based on the sequence homology, the dominant groups for up-regulated DEGs in these three categories were revealed to be metabolic process, catalytic activity and cell, respectively (Fig. 3). For down-regulated DEGs, on the other hand, metabolic processes, catalytic activity, and membranes sub-groups were revealed in each of the three main categories, respectively (Fig. 3). In addition, DEGs were mapped to the terms in the KEGG database to elucidate the enriched signal transduction pathways. All the DEGs were divided into a total of 90 KEGG pathways and the top 20 from pathway enrichment are illustrated in Fig. 4. Notably, DEGs significantly enriched carbon metabolism together with glyoxylate and dicarboxylate metabolisms (p < 0.05, Q < 0.05; Fig. 4). The three central carbon metabolism cycles in P. aeruginosa are comprised of glycolysis, pentose phosphate pathway and tricarboxylic acid cycle. It was found that a majority of enzymes involved in TCA cycle (including PA0794, PA0854, PA1581, PA1582, PA1583 and PA5445; Table 3) were repressed in ΔnirS. On the contrary, several of the enzymes contributing to the pentose phosphate pathway (including PA2261, PA2263, PA2323, PA3181, PA3182, PA3183, and PA3194) and glycolysis (PA2323, PA3193, PA3195, PA5015, and PA5016) were found activated in ΔnirS (Table 3).