There has been an increased ability to investigate human microbiota through next generation sequencing and functional assessment. This advancement has rapidly expanded our ability to study and manipulate the gastrointestinal microbiome to mitigate disease. Fecal microbiota transplantation (FMT), a therapy which broadly transfers the entire intestinal ecosystem, has been explored as a potential therapeutic in a variety of gastrointestinal, hepatic and extraintestinal conditions. The field however continues to evolve with a movement towards precision microbiome therapeutics individualizing care for various disorders. This review will describe the use of FMT, microbiota restoration and precision microbiome therapeutics focusing in gastrointestinal and hepatic diseases.