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Microbiomes are the communities of microorganisms (for example, bacteria, viruses, and fungi) that live on, in, and around people, plants, animals, soil, water, and the atmosphere. Microbiomes are active in the  functioning of diverse ecosystems, for instance, by influencing water quality, nutrient acquisition and stress tolerance in plants, and stability of soil and aquatic environments.

When new environmental conditions cause the composition of a microbiome to change, such that some microorganisms become pathogenic (capable of causing disease) or overgrowth occurs among certain microbial groups, altering the function of the microbiome, these dysfunctional microbiomes can cause visible problems. Results of dysfunctional microbiomes include coral disease, reduced agricultural crop production, and contaminated waterways.

One example is White-Nose Syndrome (WNS) in bats. White-Nose Syndrome (WNS) is a fungal disease that has caused the death of six million hibernating bats across the United States and Canada since it emerged in 2007. The USGS National Wildlife Health Center, with U.S. Fish and Wildlife Service and other partners, continues to play a primary role in WNS surveillance and research. Current projects include the collection of baseline skin microbiome data on bats to identify natural defenses and potential biocontrol agents against