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I'm confused on your use of microbiome here. Whenever I read papers for fun on the human microbiome/microbiota, they define the human microbiome as the collective genomes of the microbiota, not the microbiota itself (e.g. the first paragraph here of the paper defining the Human Microbiome Project: (Nature 449, 804-810 (18 October 2007) | doi:10.1038/nature06244; Published online 17 October 2007 or the glossary of this review: Nature Reviews Microbiology 7, 887-894 (December 2009) | doi:10.1038/nrmicro2245). Here it sounds like you're calling the organisms that live on and in people as the microbiome, where these papers make it sound like that should be referred to as the microbiota, not the microbiome. So, what does microbiome mean nowadays?

Elio replies: Best I can tell, the term microbiome was coined by the late Joshua Lederberg to denote the microbial biota of a host organism. He did not mean the genomes but the bugs themselves. But you're right, it's often used for the genomes. Confusing? Yes.See http://jb.asm.org/content/192/19/5002.full#ref-37
Thanks for this query.

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