The cost of genomic sequencing has dropped four orders of magnitude in the last decade, ushering in a new age of microbiology but also presenting challenges to bench scientists uninitiated in the analysis of big data. In this course, we will discuss how microbial genomes are generated, analyzed and exploited to provide unprecedented insights into their role in health and disease. Of particular note is the growing appreciation that microbes do not operate in isolation but form parts of larger populations and communities (microbiomes) with unique considerations for human health. Material will be presented through traditional lectures, online videos and reading, and through hands-on computer labs that provide practical experience with the software tools currently being applied to analyze these complex datasets.