Microbiome Definition

Summary

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.

Key Points

• 1

  A microbiome is an ecological community of microorganisms in a defined habitat, including their activities, interactions, and environmental context.

• 2

  The microbiota consists of the living members of a microbiome, while the microbiome is the broader community and its functional setting.

• 3

  Commonly recognized microbiome members include bacteria, archaea, fungi, algae, and protists; the status of viruses and mobile genetic elements is more controversial.

• 4

  Microbiomes are dynamic and influence the health and functioning of humans, animals, plants, and ecosystems.

• 5

  Advances in microscopy, DNA sequencing, PCR, metagenomics, and multi-omics have transformed the study of microbiomes.