Metabolic phenotyping of the cyanobacterium Synechocystis 6803 engineered for production of alkanes and free fatty acids

► Synechocystis 6803 was engineered for enhanced photosynthetic conversion of CO2 to alkanes. ► Synechocystis 6803 was engineered for accumulation of free fatty acids. ► Single-cell metabolic phenotyping was performed using SR-FTIR spectromicroscopy. ► Multivariate analysis of SR-FTIR data revealed biochemical shifts in engineered cells. ► SR-FTIR spectromicroscopy provides a high-throughput tool for screening engineered cells.