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Background  Riboflavin, an intermediate of primary metabolism, is one kind of important food additive with high economic value. The microbial cell factory  Bacillus subtilis  has already been proven to possess significant importance for the food industry and have become one of the most widely used riboflavin-producing strains. In the practical fermentation processes, a sharp decrease in riboflavin production is encountered along with a decrease in the dissolved oxygen (DO) tension. Influence of this oxygen availability on riboflavin biosynthesis through carbon central metabolic pathways in  B. subtilis  is unknown so far. Therefore the unveiled effective metabolic pathways were still an unaccomplished task till present research work.    Results  In this paper, the microscopic regulation mechanisms of  B. subtilis  grown under different dissolved oxygen tensions were studied by integrating  13 C metabolic flux analysis, metabolomics and transcriptomics. It was revealed that the glucose metabolic flux through pentose phosphate (PP) pathway was lower as being confirmed by smaller pool sizes of metabolites in PP pathway and lower expression amount of  ykgB  at transcriptional level. The latter encodes 6-phosphogluconolactonase (6-PGL) under low DO tension. In response to low DO tension in broth, the glucose metabolic flux through Embden–Meyerhof–Parnas (EMP) pathway was higher and the gene,  alsS , encoding for acetolactate synthase was significantly activated that may result due to lower ATP concentration and higher NADH/NAD +  ratio. Moreover, ResE, a membrane-anchored protein that is capable of oxygen regulated phosphorylase activity, and ResD, a regulatory protein that can be phosphorylated and dephosphorylated by ResE, were considered as DO tension sensor and transcriptional regulator respectively.    Conclusions  This study shows that integration of transcriptomics,  13 C metabolic flux analysis and metabolomics analysis provides a comprehensive understanding of biosynthesized riboflavin’s regulatory mechanisms in  B. subtilis  grown under different dissolved oxygen tension conditions. The two-component system, ResD–ResE, was considered as the signal receiver of DO tension and gene regulator that led to differences between biomass and riboflavin production after triggering the shifts in gene expression, metabolic flux distributions and metabolite pool sizes.    Electronic supplementary material  The online version of this article (doi:10.1186/s12934-017-0764-z) contains supplementary material, which is available to authorized users.

Mixomics analysis of Bacillus subtilis: effect of oxygen availability on riboflavin production