Human microbiome analysis is the study of microbial communities found in and on the human body. The goal of human microbiome studies is to understand the role of microbes in health and disease. Imbalances of the normal gut microbiota have been linked with gastrointestinal conditions such as inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS), and wider systemic manifestations of disease such as obesity, type II diabetes, and atopy.

Traditionally, studying samples from human skin, stool, or blood relied on time- and labor-intensive microbiology techniques of growing and isolating individual organisms followed by phenotypic or genotypic analysis. The throughput and cost savings of next-generation sequencing (NGS) have fueled metagenomics studies capable of surveying the genomes of entire communities, including those of unculturable organisms. These methods include:

- Shotgun metagenomic sequencing: A DNA sequencing method that enables comprehensive sampling of all genes in all organisms in a given complex microbial sample.

- 16S rRNA sequencing: A 16S ribosomal RNA gene sequencing method used to identify and compare bacteria present within a given sample.

- Microbial metatranscriptomics: Analysis of all RNAs encoded by a group of microorganisms within a complex sample.