Human microbiome

The human microbiome refers broadly to the microscopic life associated with the body and, depending on the definition, its genetic material and biochemical capabilities. It includes bacteria, archaea, fungi, viruses and other microscopic eukaryotes. The term is sometimes distinguished from microbiota, which usually refers to the organisms themselves, but usage varies across scientific fields. The microbiome is not a single uniform population: it includes communities in different anatomical habitats, as well as the interactions between those communities and their human host.

Microbial communities occur in places such as the gastrointestinal tract, mouth, skin, nasal passages and vagina. Conditions differ from site to site, so each habitat supports a distinctive mixture of organisms. Studies of healthy adults have also found substantial differences between individuals, even at the same body site; no single list of microbes describes every healthy person. Diet, environment, host biology and exposures over a person's life can all be relevant to this variation. The community can also change over time, including in response to medications and environmental influences.

Microbes associated with the body perform metabolic activities that interact with human physiology. Research describes roles in helping digest food, supporting immune-system development and limiting the establishment of some pathogens. These effects are not uniformly beneficial: outcomes depend on the organisms, their activity, the body site and the host's circumstances. Researchers have reported links between microbiome variation and a range of health conditions, but a correlation alone cannot establish whether a microbial change contributes to disease, results from it, or reflects another factor. Studies that follow people over time and examine host–microbe mechanisms are needed to clarify such relationships.

Microbiome research uses methods that can examine organisms difficult to grow in laboratory culture. DNA sequencing can identify microbial genetic material in samples, while broader metagenomic and other molecular analyses can investigate genes, transcripts, proteins and metabolites. These measurements help researchers study both community composition and possible functions, but results depend on sample collection, the body site, analytical methods and comparison groups. The U.S. National Institutes of Health's Human Microbiome Project developed shared sequence datasets and computational resources to characterize human-associated communities. Its later integrative phase combined measurements from microbes and hosts over time in studies of conditions including inflammatory bowel disease, prediabetes and preterm birth.

The field has moved from describing which microbes are present toward studying what they do and how their activities interact with the host. Even among people considered healthy, microbial communities can differ markedly, so research must account for normal variation and avoid treating one profile as a universal ideal. Observational links can generate hypotheses but do not, on their own, justify claims that a particular microbe causes illness or that altering the community will treat it. Ongoing research seeks to identify mechanisms, distinguish cause from consequence and determine when microbiome measurements can be useful in diagnosis or treatment.