The diversity of natural products is greater than that of combinatorial chemistry compounds and is similar to that of drugs. Compounds rich in sp3 carbons, such as natural products, typically exhibit high structural complexity and high specificity to molecular targets. Microorganisms can synthesize such sp3 carbon-rich compounds and can be used as excellent factories for making bioactive compounds. Here, we mainly focus on pathway engineering of two sp3 carbon-rich bioactive indole alkaloids, fumitremorgin C and terpendole E. We also demonstrate the importance of activation of secondary metabolism by focusing on tenuazonic acid, a bioactive tetramic acid compound, as an example.