The last decade has seen the emergence of “microbiome” research, which seeks to define the interactions and processes inherent to a microbial community (micro-), placed in context with the physiochemical attributes of their surrounding environment (-biome). Technological advances, and in particular, DNA/RNA sequencing and computational biology have enabled this field of research to rapidly expand, alleviated of the restrictions historically imposed by cultivation-based microbiological techniques. Many clinical and small animal studies have now established that variations in the microbiome affect host phenotype and responses to many non-communicable diseases. Microbiota transplants have also now been shown to transfer either “pathogenic” or “protective” responses to naïve hosts, further establishing the links between the microbiome and disease course. This presentation will address some of the basic concepts inherent to emergence and evolution of microbiome research, with specific reference to our collaborative projects involving clinical and nutritional studies of diabetes and pregnancy. The talk will also emphasize two principal concepts: how the field of environmental microbiology offers new insights into the role of the microbiome in health and disease; as well the needs and opportunities that can and will arise from a “return” to classical microbiology techniques, for the translation of microbiomes to medicine.