Abstract: Provided herein are methods and compositions for increasing the safety and effectiveness of a bacteriotherapy. In some aspects, a mixture of prebiotics, e.g., human milk oligosaccharides, are administered to a subject who has or will undergo a bacteriotherapy. In certain aspects, the mixture of prebiotics is administered in combination with a probiotic capable of internalizing and/or consuming the prebiotics. Also provided are methods for preparing or identifying strains of bacteria suitable for a bacteriotherapy, such as by incubating a mixture of bacteria obtained from stool in the presence of one or more of agents, e.g., human milk oligosaccharides, capable of promoting the growth of beneficial bacteria.