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From Wikipedia:

A microbiome is the totality of microbes, their genetic elements (genomes), and environmental interactions in a defined environment. A defined environment could, for example, be the gut of a human being or a soil sample. Thus, microbiome usually includes microbiota and their complete genetic elements. The human microbiome contains over 10 times more microbes than genetically human cells.^[1]

The expression “microbiome” was coined by Joshua Lederberg. In his opinion, the microorganisms should be included as part of the human genome, because of their influence on human physiology.

[1] Zimmer, Carl (13 July 2010). “How Microbes Defend and Define Us”. New York Times. http://www.nytimes.com/2010/07/13/science/13micro.html?_r=2&pagewanted=all. Retrieved 17 July 2010.