The Microbiome Analysis Core at the Harvard T.H. Chan School of Public Health was established in response to the rapidly emerging field of microbiome research and its potential to affect studies across the biomedical sciences. The Core’s goal is to aid researchers with microbiome study design and interpretation, reducing the gap between primary data and translatable biology. The Microbiome Analysis Core provides end-to-end support for microbial community and human microbiome research, from experimental design through data generation, bioinformatics, and statistics. This includes general consulting, power calculations, and selection of data generation options, as well as analysis of data from amplicon (16S/18S/ITS), shotgun metagenomic sequencing, metatranscriptomics, metabolomics, and other molecular assays. The Microbiome Analysis Core has extensive experience with microbiome profiles in diverse populations, including taxonomic and functional profiles from large cohorts, qualitative ecology, multi’omics and meta-analysis, and microbial systems and human epidemiological analysis. By integrating microbial community profiles with host clinical and environmental information, we enable researchers to interpret molecular activities of the microbiota and assess its impact on human health.