microbiomes

Microbiomes are complex communities of microorganisms that inhabit a defined environment, together with their genetic material and the interactions among the organisms. The term is used for microbial assemblages on and within living hosts as well as in external environments such as soil, oceans, and built surfaces.

Commonly studied examples include the human microbiome, which encompasses microbial communities in the gut, skin, mouth, and other sites. Microbial communities consist of bacteria, archaea, fungi, viruses, and other microscopic organisms, in addition to the biomolecules they produce and responsive networks they form.

These communities influence numerous processes: they help degrade dietary components and extract nutrients, synthesize vitamins, educate and modulate the immune system, and resist colonization by pathogens. They also participate in biogeochemical cycles in the environment and can affect the health and productivity of plants and animals.

Scientists study microbiomes using culture-independent methods such as metagenomics and 16S rRNA gene sequencing, as well as metatranscriptomics, metaproteomics, and metabolomics. These approaches reveal composition, gene potential, and activity, though translating associations into causality remains challenging.

Microbiomes are shaped by multiple factors, including diet, antibiotics, age, genetics, geography, and lifestyle. They can be stable yet exhibit plasticity in response to perturbations, with dysbiosis describing dysregulated or imbalanced states linked to disease or dysfunction.

Applications include interventions such as probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, as well as microbiome-informed strategies in medicine, agriculture, and environmental management. Ongoing research aims to define core microbiomes, understand host–microbe interactions, and develop standardized methods for comparison and interpretation.