The human microbiota is the collection of microorganisms—bacteria, archaea, viruses, fungi, protozoa, and helminths—that populate the human body. They are emerging as an important feature of human health and disease. Currently, access to the genomic data of human cells and of microbiota (microbiomes) is more affordable and accessible than ever before. A major challenge is to unravel how we integrate microbiome data into precision medicine approaches for the prevention, diagnosis, and treatment of diseases such as cancer. The gastrointestinal (GI) tract is densely populated with microorganisms. Colorectal cancer (CRC) is the third most prevalent cancer worldwide. It is increasing in individuals less than 50 years old and is associated with specific dietary factors and eating patterns that affect the gut microbiota. Therefore, CRC seems ripe for microbiome-based prevention, diagnostics, and therapeutics.