Microbiome. Microbes are the small organisms that we can just barely see under a microscope, like bacteria, fungi, viruses... And these microbes live everywhere. They live in the soil, they live in the water, and they live in and on our body. The microbiome is a new term that refers to all of the genetic material found in an individual microbe such as one of these bacteria or fungi or viruses. So if we think about the entire DNA sequence of a microbe, that is the microbiome.Julie A. Segre, Ph.D.