Investigating Human Diseases with the Microbiome: Metagenomics Bench to Bedside is a summary of underlying principles for human health and disease studies from a microbiome point-of-view. From birth to old age, microbiomes in fecal, oral/nasal, vaginal, and skin samples contain important information that can predict disease risks in the future. Tissue samples also contain microbes that are relevant for diseases. The microbiome connects genetic and environmental factors and is poised to greatly facilitate precision medicine, including prevention, diagnosis and effective treatment of many complex diseases. Based in traditional microbiology and adding a more wholistic view of the advent of high-throughput sequencing, this reference poses the key questions of the total number of microbial cells and their distribution in the human body while also considering concepts from macroecology and from causal reasoning. An entire chapter is dedicated to methods, providing hands-on information for important considerations when collecting samples for metagenomic studies.