What Is a Microbiome?

A microbiome is the full community of microorganisms occupying a defined habitat, together with their collective genomes and the chemical environment they create and inhabit. The habitat may be a body site such as the human gut or skin, a plant root zone, a soil horizon, an ocean depth, or an engineered system such as a bioreactor or a wastewater plant. The community includes bacteria, archaea, fungi, protists, and viruses, and the term covers the genes and metabolites they contribute as well as the organisms themselves. Microbiome research therefore differs from classical microbiology in unit of study: the object of interest is an assemblage and its emergent function rather than a single isolated species.

The field expanded rapidly once high-throughput DNA sequencing made it possible to survey communities without culturing them, since most environmental and host-associated microbes do not grow under laboratory conditions. Analysis draws on microbial ecology for its conceptual framework, on genomics for its measurements, and on statistics and machine learning for interpretation of high-dimensional compositional data.

Composition, Diversity, and Stability

A microbiome is described by which taxa are present, in what relative abundance, and how those quantities vary. Within-sample variety is summarized as alpha diversity, while between-sample difference is summarized as beta diversity, usually with distance measures that account for phylogenetic relatedness. Human body sites differ sharply from one another: the colon supports a dense anaerobic community dominated by Bacteroidota and Bacillota, while skin communities are sparser and structured by sebaceous, moist, or dry conditions. The NIH Human Microbiome Project established reference ranges for healthy adults across multiple body sites and found substantial variation between individuals at the species level alongside consistency in the metabolic functions encoded. Communities are shaped by diet, host genetics, age, medication, and colonization history, and they can shift abruptly after antibiotic exposure before partially recovering.

Measurement and Analysis

Two sequencing strategies dominate. Marker gene surveys amplify the bacterial 16S ribosomal RNA gene or the fungal internal transcribed spacer region and provide inexpensive taxonomic profiles at coarse resolution. Shotgun metagenomic sequencing reads all DNA present, resolving species and strains and revealing gene content directly. Because sequencing yields relative rather than absolute abundances, the resulting data are compositional, and statistical methods must account for that constraint to avoid spurious correlations. Multi-omic designs add transcriptomics, proteomics, and metabolomics so that observed community structure can be linked to activity. The second phase of the NIH effort, reported as the Integrative Human Microbiome Project, followed participants longitudinally across pregnancy, inflammatory bowel disease, and prediabetes to capture dynamics rather than single snapshots.

Host Interactions and Health

Resident microorganisms perform functions the host genome does not encode, including fermentation of dietary fiber into short-chain fatty acids, synthesis of vitamin K and several B vitamins, primary bile acid conversion, and competitive exclusion of pathogens. They also train the immune system, and germ-free animals show clear developmental deficits in gut-associated lymphoid tissue. Departures from a typical community structure, often labeled dysbiosis, have been associated with inflammatory bowel disease, obesity, type 2 diabetes, colorectal cancer, and response to immunotherapy. Early findings from the project, summarized when NIH defined the normal bacterial makeup of the body, described a healthy adult as carrying trillions of microorganisms that outnumber human cells by about ten to one, a ratio that later cell-counting work revised down to roughly parity.

Applications

Microbiome research has applications in a wide range of fields, including:

• Clinical medicine, including fecal microbiota transplantation for recurrent infection
• Drug development and pharmacology, where microbial metabolism alters dosing
• Nutrition science and the design of prebiotic and probiotic products
• Agriculture, through soil and rhizosphere management and livestock feed efficiency
• Environmental engineering, including wastewater treatment and bioremediation
• Forensic and public health surveillance from environmental sampling