Microbiome Science and Research

Microbiome Definition

A microbiome is the community of microorganisms living together in a particular habitat, along with their interactions, activities, and surrounding environmental conditions. The term was defined by Whipps and colleagues in 1988 as a characteristic microbial community occupying a reasonably well-defined habitat with distinct physical and chemical properties. This definition emphasizes that a microbiome includes not only the organisms themselves but also their ecological functions and interactions, such as communication, metabolite production, cooperation, competition, and biofilm formation. The microbiota refers specifically to the living organisms that form a microbiome, including bacteria, archaea, fungi, algae, and small protists; the inclusion of viruses, phages, plasmids, and other mobile genetic elements remains debated. Microbiomes occur in humans, animals, plants, oceans, soils, and other environments, where they can strongly influence health, physiology, behavior, adaptation, and ecosystem functioning. Modern sequencing, metagenomics, and other omics technologies have revealed that most microorganisms are beneficial or essential rather than harmful and have expanded microbiome research beyond the study of infectious disease.

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Microbiota and Microbiome Distinction

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