In alternative embodiments, provided are products of manufacture and methods for treating, ameliorating and preventing diseases and conditions related to infected or dysfunctional mucosal surfaces, including mucosal surfaces in the gastrointestinal (GI) tract,
respiratory tract, and other mucosal surfaces, for example, mucosal surfaces in the
stomach,
nasal sinuses, nasopharyngeal area, lungs, bladder or the
vagina. Provided are methods and products of manufacture for preparing the GI tract for a microbiota engraftment, then infusing a colonic microbiota engraftment, for example, a
fecal microbiota transplant (FMT). In alternative embodiments, provided are methods and products of manufacture for mechanical disruption of a
biofilm followed by the chemical and / or biologic
dissolution of a
mucus layer or a
biofilm, and subsequent implantation of FMT material into or onto a mucosal surface such as a GI tract. In alternative embodiments, provided are delivery devices which permit the FMT material to reach the various mucosal surfaces, for example, mucosal surfaces in the GI tract. In alternative embodiments, provided are methods and products of manufacture for replacing an individual's
microbiome, where the individual's
microbiome may be infected, including replacing the individual's
microbiome in colonic, intestinal, gastric, respiratory or vaginal spaces or environments, with that of a healthy or not infected microbiome, where the healthy or not infected microbiome can be donor-derived or cultured. Provided herein are methods for the treatment, amelioration and / or prevention of numerous conditions characterized by an in situ microbiome super-infection, including microbiome super-infections, for example, conditions characterized as gastrointestinal (GI)
disease.