Ever since its modern conception as a medical discipline, the study of microorganisms has paralleled the many technological advances in microbiology. In the 17th century, the inventor of the microscope, Antony van Leeuwenhoek, was also the first to describe–in the plaque of his own gums-the millions of microorganisms (or “animalcules”) that reside within us. It is that multitude of microbes populating most human body cavities and surfaces, including its genetic and enzymatic composition, what defines our microbiome1.

For centuries, the role of the microbiome as potential determinant of health and disease has been rather ignored. This has been true in most fields of human research, but particularly so in autoimmune and rheumatic conditions. The reasons are multifactorial. Chief among those was the advent of the Koch’s postulates in the late 1800’s, which exerted a profound influence on how investigators thought about causality in Medicine2. Unbeknownst at the time, however, was the fact that asymptomatic carriers are a common feature of many infectious diseases and that several microorganisms are fastidious in nature with complex nutritional requirements in order to grow. The latter fundamentally prevented the study of bacteria within the context of a dynamic biological community, the role of commensal taxa, the downstream molecular events and the resulting immune interactions between microorgansims and their host.