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The term "Microbiome" is being used in two ways; either to denote all microbes at a site or all their genomes.
Both can't be right, so let's have a poll!
(as of 2023, the poll is defunct, but we posted the results here)
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In the early days when the HMP was being formed, the NIH officially defined the human microbiome as 'all of the microorganisms and their genes and genomes which make up the microbial communities that inhabit the human body'. This definition was meant to reflect that we were not just considering microbial composition but also the genetic potential of these communities. Of course what this does not reflect is any relationship between the human host and its microbial inhabitants. This is where the 'human metagenome' (ala Jeff Gordon) does a better job of capturing the host/microbial community ecosystem.
Elio replies:
I will be posting the results of the poll soon. In the meanwhile, I am thankful to Lita for this information. I'm glad that the NIH has an official definition of microbiome. However, as Lita points out there is still room for discussion. For one thing, to say that the microbiome consists of "all the microorganisms and their genes" seems like a tautology or something. Of course the organism carry their genes. It goes without saying.
Posted by: Lita Proctor | November 15, 2013 at 08:03 AM