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Human gut microbiota plays an important role in health, broadly influencing metabolism to the immune system and drug resistance to pathogenic colonization. Since antibiotic resistance is on the rise, and wide-spectrum antibiotics are known to have deleterious effects on microbial biodiversity targeted therapeutic interventions must be made. Bacteriophages are viruses that are commonly recognized to have a high level of specificity, targeting only the intended bacterial species without disrupting the overall microbial community. Advancements in genomics, bioinformatics, and synthetic biology led us to the identification and design of phages, capable of precisely targeting specific pathogens. In this review article, we aim to discuss both the challenges and opportunities of integrating phage therapies into clinical practice, discussing the limitations of traditional therapy as it pertains to the manipulation of the gut microbiome.