Abstract: The present disclosure provides technologies for modulating microbiome of mammalian subjects (e.g., human subjects). The present disclosure, among others, provides therapeutic compositions and methods of using the same, wherein the therapeutic compositions comprising an engineered population of therapeutic bacteria that (i) are non-pathogenic and commensal in a subject to be administered; and (ii) are resistant to one or more target bacteriophages. In some embodiments, such therapeutic compositions can be useful for treatment of subjects suffering from or susceptible to a microbiome-dysfunction-associated disease, disorder, or condition (e.g., inflammatory bowel disease).