What is the microbiome? The microbiome is a community of bacteria, fungi, viruses and other microbes that live inside your body and on its surface. Just as in a community of people, you’ll find both good and bad actors: Some of the microbes, like the gut bacteria that help you digest food, are beneficial, while others, like certain viruses, can be dangerous. Everyone’s microbiome differs, depending on your age, gender, diet and immune system. And the types of microbes on one part of the body may be different from those on another.