The present disclosure relates to compositions and methods for treating autism spectrum disorder (ASD) by restoring an ASD patient's gut microbiota. These methods can be used with ASD patient with or without ongoing gastrointestinal symptoms. Provided here is a method for modulating the abundance of one or more gut microorganisms in a subject in need thereof, said method comprising administering to said subject a therapeutically effective amount of a pharmaceutical composition comprising a fecal microbe preparation to achieve at least a 2-fold change of the abundance of said one or more fecal microorganisms, wherein said one or more gut microorganisms are selected from the group consisting of Bifidobacterium, Prevotella, Desulfovibrio, Copprococcus, Clostridium, and Bacteroides.