Abstract In the past decade, there has been a remarkable growth in the interest and enthusiasm for microbiome research. The microbiome includes bacteria, viruses, fungi, and parasites; our microbes cover all parts of our body. Researchers from many disciplines are now considering the role of microbiota and its relationship to development, physical health, and mental health. The multidisciplinary nature of ongoing research efforts is advancing our knowledge base at a fast pace. The current attention to tool development for analysis beyond bacterial composition will help scientists interpret the relationship between microbes, health, and disease. This article provides an introduction to host–microbe interactions based on animal and clinical research focused on the gut microbiome.