Microbial communities exist throughout the biosphere including the associations they form with humans, plants and animals. Understanding the diversity and genetic complexity of these communities, along with the interactions they undertake both within communities and with their environment has given rise to the concept of the study of the microbiome. With improvements in molecular biology, computational power, and high throughput technologies such as the advent of next generation sequencing, new opportunities exist to study the microbiome from multiple environments including their role in human health and disease. However, in order to maximize the information we can realize from these data types, careful considerations need to be made in terms of study design, and new tools and approaches are needed for data generation, analysis and interpretation. This talk will provide an overview of these topics using examples from microbiome studies.