Background: Gut microbiome comprises a diverse microbial community, including bacteria, viruses, and fungi, which play a crucial role in human health. These microbes contribute to host well-being by producing beneficial compounds such as short-chain fatty acids and other metabolites that help maintain microbial homeostasis. Recent advancements in high-throughput sequencing techniques have identified key microbes crucial for human health and revealed that an imbalance in these communities—known as dysbiosis—can lead to various diseases, including inflammatory bowel disease (IBD), Crohn’s disease, colorectal cancer, type 2 diabetes, and liver diseases. Aim: This review aims to provide a comprehensive overview of emerging microbiome-based therapeutic strategies, including fecal microbiota transplantation (FMT), prebiotics, probiotics, next-generation probiotics, synthetic microbiome transplantation, and microbiome editing therapies, as potential interventions to restore gut microbial balance and improve health outcomes. Relevance for patients: Microbiome-based therapies have emerged as promising tools for restoring gut homeostasis and managing microbiome-associated diseases. Approaches such as FMT have shown clinical benefits in conditions such as IBD, Clostridium difficile infection, and cancer immunotherapy. Understanding these therapies may guide future personalized treatments aimed at improving patient outcomes through modulation of the gut microbiome.