In microorganisms, different from primary metabolism for cellular growth, secondary metabolism is for ecological interactions and stress responses and an important source of natural products widely used in various areas such as pharmaceutics and food additives. With advancements of sequencing technologies and bioinformatics tools, a large number of biosynthetic gene clusters of secondary metabolites have been discovered from microbial genomes. However, due to challenges from the difficulty of genome-scale pathway reconstruction and the limitation of conventional flux balance analysis (FBA) on secondary metabolism, the quantitative modeling of secondary metabolism is poorly established, in contrast to that of primary metabolism. This review first discusses current efforts on the reconstruction of secondary metabolic pathways in genome-scale metabolic models (GSMMs), as well as related FBA-based modeling techniques. Additionally, potential extensions of FBA are suggested to improve the prediction accuracy of secondary metabolite production. As this review posits, biosynthetic pathway reconstruction for various secondary metabolites will become automated and a modeling framework capturing secondary metabolism onset will enhance the predictive power. Expectedly, an improved FBA-based modeling workflow will facilitate quantitative study of secondary metabolism and in silico design of engineering strategies for natural product production.

Monascus-fermented cheese (MC) is a new type of mold-ripened cheese that combines a traditional Chinese fermentation fungus, Monascus purpureus M1, with Western cheese fermentation techniques. In this study, the compositions of the volatile aroma compounds in MC were analyzed during a 30-day ripening period using SPME-Arrow and GC-O-MS. The activity of esterase in MC, which is a key enzyme catalyzing esterification reaction, was determined and compared with the control group (CC). Next, sensory analysis was conducted via quantitative descriptive analysis followed by Pearson correlation analysis between esterase activity and the key flavor compounds. A total of 76 compounds were detected. Thirty-three of these compounds could be smelled at the sniffing port and were identified as the key aroma compounds. The esterase activity in MC was found to be 1.24~1.33 times that of the CC. Moreover, the key odor features of ripened MC were alcohol and fruity flavors, considerably deviating from the sour and cheesy features found for the ripened CC. Furthermore, correlation analysis showed that esterase activity was strongly correlated (|r|> 0.75, p < 0.05) with various acids such as pentanoic and nonanoic acids and several aromatic esters, namely, octanoic acid ethyl ester and decanoic acid ethyl ester, revealing the key role that esterases play in developing the typical aroma of ripened MC.