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AIM Investigate the effects of different nitrogen sources on the metabolic characteristics of Sphingomonas paucimobilis during gellan gum (GG) production were helpful for developing optimized conditions that are widely applicable to all GG production processes. METHODS AND RESULTS We compared the effects of organic nitrogen (ON) and inorganic nitrogen (IN) sources during GG production using transcriptome sequencing. Our results showed that compared with the IN source, the ON source effectively improved the cell number and GG production of S. paucimobilis during fermentation. There were significant differences in gene transcription levels between the ON and IN groups at different fermentation times. CONCLUSIONS The transcriptional levels of multiple genes in the pathways from α-D-glucose-1P to glyceraldehyde-3P were reduced in the ON group, whereas those of multiple genes in the pathways from glyceraldehyde-3P to acetyl-CoA were significantly enhanced in the ON group after 12 h of fermentation. The transcription levels of multiple genes participating in the citrate cycle and upstream of fatty acid metabolism pathways were significantly enhanced in the ON group after 12 h of fermentation. Except for the transcripts per million (TPMs) of pgm and rfbA genes in ON, which were significantly higher than those in IN at 12 h after fermentation, the TPMs of the majority of genes in ON were significantly lower than those in IN. The transcription levels of genes participating in the transformation of N-acetyl-D-glucosamine (GlcNAc) to UDP-N-acetyl-alpha-D-glucosamine (UDP-GlcNAc) were enhanced in the ON group during the fermentation process.