Gastrointestinal metagenome is the study of the collective genetic material of the microorganisms living in the human gastrointestinal tract. It focuses on the composition and diversity of the microbiota, the metabolic pathways, and the interaction between the microbial population and their host. The human gut microbiota is composed of over 1000 different species and is essential for human health. It plays an important role in digestion, absorption of nutrients, regulation of the immune system, and protection against pathogens. The gastrointestinal metagenome is a rapidly growing field of study that has the potential to provide insight into the mechanistic basis of many diseases. The analysis of the metagenome is providing a better understanding of how the microbial community interacts with its host and its role in health and disease. Investigations into the gut microbiota have identified links between the microbial composition and diseases such as inflammatory bowel disease, obesity, and diabetes. In addition to microbial composition, the microbial metabolic pathways and their interactions with the host are also important. The metagenome can provide a better understanding of the host-microbe metabolic interactions and the role of the microbiota in the development and progression of diseases.