Among all areas of development in synthetic biology, microbiome therapy is one of the most rapidly advancing and highly anticipated areas of technology. As the science community uncovers the close relationship between microbial ecology and human health, microbiomes are regarded as a “second genome” apart from the human genome, with extensive effects on gastrointestinal health, chronic diseases, cancer, and psychological disorders. As a result, clinical applications of microorganisms are becoming increasingly prevalent, ranging from therapeutics, diagnostics,  disease prevention, and novel carriers of therapeutic molecules. Companies and institutions are testing these in clinical trials, and regulatory agencies have approved some for marketing as derivative pharmaceutical products. With the main focus on microbiome therapy, this feature article will provide an in-depth overview of this promising technology's technical principles, clinical applications, and future trends.