Microbiome

A microbiome is the community of microorganisms that inhabit a defined environment and their collective genetic material. The term is widely used for the human microbiome, especially the gut, but it applies to any habitat, including soil, oceans, and plant or animal bodies.

In humans, the microbiome includes bacteria, archaea, viruses, and fungi. The gut microbiome is the most studied and has a major influence on digestion and metabolism; other body sites host distinct communities, such as the skin, oral cavity, and vagina.

The microbiome's functions extend beyond digestion. Microbes assist in extracting nutrients from food, synthesize vitamins, train the immune system, and help maintain the integrity of mucosal barriers. The collective genomes, or metagenomes, expand the host's metabolic repertoire beyond what its own genes encode.

Composition is shaped by factors including diet, antibiotics, age, mode of birth, geography, and lifestyle. Microbiomes are dynamic, changing with illness, weight, and environment, and tend to drift toward individual-specific configurations.

Dysbiosis, or imbalances in microbial communities, has been associated with diseases such as inflammatory bowel disease, obesity, allergies, and infections. Causality is complex; microbiome-targeted interventions—dietary changes, probiotics, prebiotics, and fecal microbiota transplantation—are areas of active research.

Methods in microbiome research include 16S ribosomal RNA gene sequencing for taxonomic profiling and shotgun metagenomics for functional potential. Culturing remains limited, whereas computational analyses and reference catalogs enable large-scale comparisons across individuals and environments.

Beyond humans, environmental microbiomes influence soil fertility, plant health, and biogeochemical cycles. Studying microbiomes across habitats helps reveal ecological interactions and informs medicine, agriculture, and environmental management.