What does the term microbiome mean? And where did it come from? A bit of a surprise ..

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BIOLOGICAL SCIENCES What does the term microbiome mean? And where did it come from? A bit of a surprise .. JONATHAN EISEN READ REVIEWS ✎ WRITE A REVIEW CORRESPONDENCE: jaeisen@ucdavis.edu DATE RECEIVED: “Microbiome” is such a hot term these days. And one key question many ask is “what does it mean?” A related question is – “where did the term come from?” I tried to tackle this many years ago on my blog with a post: The human microbiome – term being used in many ways – but at least it is getting some \npress. Basically my main point was that it seemed that the term “ microbiome” then should be used to refer to the collection of genomes of microbes in a system and that “microbiota” should be used to refer to the collection of organisms. Some key quotes from that post: June 10, 2015 DOI: 10.15200/winn.142971.16196 ARCHIVED: April 22, 2015 CITATION: Jonathan Eisen, What does the term microbiome mean? And where did it come from? A bit of a surprise .., The Winnower 2:e142971.16196 , 2015 , DOI: 10.15200/winn.142971.16196 © Eisen This article is distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and redistribution in any medium, provided that the original author and source are credited. Well, the human microbiome is all over the news recently thanks to a new paper on the diversity and biogeography of microbes in human saliva. My only complaint is that I and Stoneking and many others have unfortunately made a mess of the terminology. The “microbiome” was originally used to refer to the collection of the genomes of the microbes in a particular ecosystem. And the terms “microbiota” was used to refer to the actual organisms. Since Stoneking et al did not survey the genomes, they surveyed rRNA (which really at best tells you about what types of organisms are present) then they should have used microbiota riight? (And if they had I would not have been searching for the genomics component of their work). Not so fast, even the person who coined the term microbiome (Josh Lederberg) who originally seemed to use it to refer to all the genomes of the microbes also used the term ambiguously (e.g., in one paper he sad “the microbiome flora” meaning I guess the microbiota. I note, everyone seems to cite A paper by Lederberg called “Infectious History” in Science (Science 14 April 2000:) as the place he used microbiome but I cannot find the term there. I did however find the term in a paper in 2001 by Lora Hooper and Jeff Gordon (Commensal Host-Bacterial Relationships in the Gut Science 11 May 2001: Vol. 292. no. 5519, pp. 1115 – 1118). The Nobel laureate Joshua Lederberg has suggested using the term “microbiome” to describe the collective genome of our indigenous microbes (microflora), the idea being that a comprehensive genetic view of Homo sapiens as a life-form should include the genes in our microbiome (4). And reference 4 is “Personal communication” Anyway, others have taken the term microbiome and run with it because it does conjure up to many “microbial biome” which could be used to refer to all the microbes in a system. I prefer the original definitions with microbiota being the organisms and microbiome being the collective genomes of all the organisms. EISEN The Winnower APRIL 22 2015