The microbiome consists of bacteria, viruses, fungi, parasites, and protozoa, although most research to date has focused on the bacterial microbiome. Commensal bacteria cover all surfaces of the human body. Differences in the composition of the bacterial microbiome are observed across body sites, and differences are observed between individuals. Understanding the factors that influence individual differences in a person's microbiome is essential in determining the importance of the microbiome to health and disease. Genetics, sex, age, diet and other factors influence microbiome composition and function. Recent advances in sequencing tools and bioinformatics to study the microbiome has provided an abundance of information related to the healthy microbiome. Some key taxa have been identified that are present in most individuals and understanding the biology of these taxa adds to the ability to use microbiome measurements as biomarkers of health, and to consider microbiome-targeted approaches to maintain gut homeostasis and overall health.