The totality of all microorganisms, i.e., all bacteria, fungi, viruses, and protozoa, is called the microbiome. Especially the human microbiome is gaining more and more interest due to its important contributions to health. The largest human microbiome is in the intestine. However, the skin, oral cavity, nasal cavity, paranasal sinuses, and many other body sites in direct or indirect contact with the outside world also carry a microbiome. Not only humans have a microbiome, but other organisms also carry microorganisms, such as plants. The microorganisms in their roots or seeds influence the growth and health of the plant. Advances in sequencing technologies facilitated the determination and analysis of the totality of these microorganisms.