Trillions of microorganisms inhabit the gastrointestinal tract, comprising the gut microbiome. Currently, we understand the many roles the gut microbiome plays in metabolism, immune function, and human health. We knew little about how it interacted with human physiology, but advances in metagenomics, metabolomics, and systems biology have created opportunities to understand host-microbe bi-directional interactions. We opened the door to considering the gut microbiome as a next-generation therapeutic target for chronic diseases. This review summarizes the evidence from clinical trials that manipulate gut microbiome interactions through dietary modification, probiotic supplementation, synbiotics, and human fecal microbiota transplantation. Clinical trials conducted to assess evidence for obesity, type 2 diabetes, and chronic kidney disease consistently demonstrate that microbiome modulation can improve metabolic health outcomes with reductions in systemic inflammation. In other autoimmune and inflammatory conditions, such as rheumatoid arthritis and inflammatory bowel disease, gut microbiome-assisted modification is performed to restore immune tolerance and mitigate the severity of disease progression. In other chronic disease conditions, the gut-brain axis is emerging. In Parkinson’s and Alzheimer’s disease, interventions have shown that microbiome modulation may help reduce neuroinflammation and cognitive impairments. The modulation of gut microbiota also supports improved outcomes associated with cancer immunotherapy and augmenting treatment efficacy. Although promising results have been achieved, the path from microbiome research to clinical translation presents several challenges, including considerable interindividual variability, a lack of standardization in protocols, and a shortage of mechanistic biomarkers. Future research will need to place a higher emphasis on broader trials, randomized controlled trials, and the combination of multi-omics approaches and precision strategies (e.g., precision nutrition and engineered probiotics) to yield specific therapeutic frameworks. In conclusion, this review highlights the potential clinical applications of microbiome modulation, as well as several favorable factors that must be considered for its integration into clinical practice.