On one side, we essentially have single-celled living things whose genetic material floats freely inside them. You may remember learning in school that there are two major empires of life. But the microbiome is not only made up of bacteria. This microscopic ecosystem, known as the microbiome, may play important roles in our health but scientists are only now beginning to understand very small elements of it. Much has been written about the bacteria that live inside our gut. Scientists who study tiny living things are facing their own type of dark matter: invisible microbes that are indirectly detected. “Dark matter” is the phrase coined for the matter that is implied to be present in the universe based on physicists’ calculations but that cannot be seen yet. There is a kind of dark matter inside our intestinal tract.