In the human body there are many microorganisms with a variable genetic content. These microorganisms play an important role in the metabolism, homeostasis, immune system and generally human health. Over the millions of years, different microorganisms adapted to each other, and different environmental communities formed on Earth. Microbial communities, known as microbiome, could exist in living or non-living environments, such as human body and plants, as well as in soil, oceans, and air. The main purpose of microbiome engineering is mostly human microbiome and is now used in the treatment of diseases such as Clostridium difficile infection, inflammatory bowel disease, obesity, etc. The research data in this thesis were collected from the main medical article sources including Web of science, Google scholar, PubMed and Scopus. Articles on microbiome which published during 2010-2019 were reviewed. The widespread impacts of the microbiome on the ecosystems and the increased attention to microbiome recognition are factors contributing to the creation of microbiome engineering science, and recent advances in genome sequencing and metagenomic science have made microbiome analysis apart from cultivation process. Microbiome engineering has advantages and disadvantages. So, according to the positive aspects and efforts to increase applications, this science could lead to advances in microbial engineering, and have positive effects on human health. Although microbiome engineering is a new field, there has been lots of progressions in recent years that can be an important strategy for improving human health by microbial manipulation leading to the changing of microbial population.