1. A method for treating or clearing a Clostridium difficile infection (CDI) in a subject in need thereof, the method comprising administering to the subject a single dose of a pharmaceutical composition comprising a freeze-dried fecal microbe preparation derived from a stool of a healthy human donor, wherein (a) a relative abundance of Proteobacteria in the subject's stool decreases by at least 40%, (b) a relative abundance of Firmicutes in the subject's stool increases by at least 50%, or (c) a relative abundance of Bacteroidetes in the subject's stool increases by at least 50%, within 3 to 6 days from administering the single dose relative to a baseline abundance immediately prior to administering the single dose, wherein the method achieves a CDI clearance rate as determined by the absence of detectable C. difficile toxin B DNA in the stool of the subject.