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August 2, 2018

You’ve heard of tiny houses, introducing (really) tiny communities - microbiomes!

The EarthWord: Microbiome


mycobiome (fungal community)
Mycobiome (fungal community) from a resistant bat species growing in culture (a swab from the bat's skin was streaked across the agar surface in lines). Pink and white structures are colonies of different yeast species from the wing of the bat growing on laboratory medium.(Credit: Jeff Lorch, USGS. Public domain.)

Definition:  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. 


"micro" - from the Greek 'mikros' means small; in this usage it refers to microorganisms, i.e., organisms so small you need the magnification of a microscope to see them

biome" - from Ancient Greek 'bios' meaning life and 'ome' a back-formation from mitome, reinforced by chromosome; the combination biome was coined in 1916 and means any major regional biological community such as a forest or desert

Use/Significance in the Earth Science Community:

  • 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.
  • The National Microbiome Initiative aims to advance the understanding of microbiome behavior and enable protection and restoration of healthy microbiome function. It has a 5-year goal of promoting the integrated study of microbiomes across different ecosystems.  Federal microbiome scientists across the U.S. Government recently released a strategic plan for microbiome research (2018-2022).


  • Working with partners at the Great Lakes Commission and several universities, USGS scientists are developing control methods and management strategies targeting the symbiotic relations between invasive plants (for example, Phragmites australis, a reed) and their microbiomes.
  • USGS scientists working with U.S. Fish and Wildlife Service and other partners, play a primary role in White Nose Syndrome surveillance and research. Current projects include the collection of baseline skin microbiome data on bats to identify natural defenses and potential biocontrol agents against WNS.
  • Gulls in urban areas of Alaska were more likely to be carriers of antibiotic resistant strains of the bacteria Escherichia coli (E. coli) than gulls from remote areas according to findings by USGS researchers working with academic colleagues from Sweden. Although E. coli is a normal part of gull gut microbiomes, finding multi-drug resistant strains in wild birds suggests transmission from human waste, such as landfills or wastewater, and raises questions about the risk for re-transmission in areas where people and gulls interact.
  • Hundreds to thousands of feet deep in the ocean, more than 3,000 species of deep-sea corals have been identified, and more continue to be discovered. Corals, which can be hundreds of years to centuries old, provide essential habitat for commercial fish species and harbor an array of biodiversity. Researchers at the USGS are identifying baseline microbiomes of deep-sea coral species for conservation and management of these natural resources. Coral habitats are particularly sensitive to climate change and human activities, such as energy exploration, fishing, and mining, that are moving into greater ocean depths making baseline assessments critical knowledge.

To learn more about USGS microbiome research, check out the fact sheet, USGS microbiome Research  


Hungry for some science, but you don’t have time for a full-course research plate? Then check out USGS Science Snippets, our snack-sized science series that focuses on the fun, weird, and fascinating stories of USGS science.