In alternative embodiments, provided are products of manufacture for microbiome transplantation and engraftment, including fecal microbiota transplantation (FMT) delivery devices, and methods for using them, including methods for replacing an individual's gastrointestinal (GI), e.g., colonic, microbiome, and methods for the treatment, amelioration or prevention of an in situ microbiome space, or a gastrointestinal (GI) disease, infection or condition or a disease or condition caused by, initiated by or exacerbated by a pathological microbiome, e.g., pathological GI or colonic microbiome. In particular a method for microbiome transplantation and engraftment in an individual in need thereof, the method comprising: removing of some or all colonic fecal material from the colon of the individual in need thereof by washing out colonic fecal material from the colon, wherein said washing out comprises administering a formulation comprising a biofilm dissolving or disrupting agent to the colon, and administering a FMT material, liquid, formulation or solution, or a normal microbiome, to the individual in need thereof.