This application provides compositions, e.g., formulations, used for gastric, gastrointestinal and/or colonic treatments, and methods for making, storing and using them, including formulations that effectively preserve microbial cell viability during freeze-thaw or freeze-drying. Compositions provided herein are useful for treating various diseases or conditions such as autism spectrum disordor, Crohn's Disease, ulcerative colitis, irritable bowel syndrome, and recurrent or primary C.difficile infection.