text: The second phase of the $170 million Human Microbiome Project was focused on integrating patient data to different omic datasets, considering host genetics, clinical information and microbiome composition. The phase one focused on characterization of communities in different body sites. Phase 2 focused in the integration of multiomic data from host & microbiome to human diseases. Specifically, the project used multiomics to improve the understanding of the interplay of gut and nasal microbiomes with type 2 diabetes, gut microbiomes and inflammatory bowel disease and vaginal microbiomes and pre-term birth.