Methods and compositions that can be used to modulate serotonin level in a subject are disclosed herein. In some embodiments, the methods include adjusting the composition of gut microbiota in the subject. Also disclosed are methods of adjusting the level of one or more serotonin-related metabolites to modulate serotonin biosynthesis in a subject, and methods for treating serotonin-related diseases, for example disorders caused by serotonin deficiency.