Tuesday, March 03, 2009

The human microbiome - term being used in many ways - but at least it is getting some press

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. The paper "Global diversity in the human salivary microbiome Global diversity in the human salivary microbiome" was by Mark Stoneking's lab and is in press in Genome Research (I am following my brother's trend and not putting a link here since the paper in non Open Access). In the paper Nasidze et al report on the use of PCR and sequencing of the rRNA genes from bacteria in human saliva from 120 people. They compare and contrast the samples (14000 sequences in total) and make some conclusions about the connection between bacterial diversity and genetic biogeography of the people from which the samples came.

And this has been covered in the press a bit here and there including
Get ready for much more in the next few years about microbes in and on us (see my discussion of this previously).

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.

I have been as guilty as others in mixing up the terms but in the future I plan to push for "microbiome" to be an omics word and not a biome word and for microbiota to be the biome word. That way if you skim a paper or title you might be able to better guess what it is about.


  1. One of the major problems with the use of "microbiome" to describe 16S-based data is that 16S analysis cannot differentiate bacteria (or archaea) that are closely related but differ by phages, etc. In other terms, 16S ignores a major component of the microbiome which is the "mobilome" or the "horizontal variome" (sorry, a double-omic sin).

    The Human Microbiome Project is leading to the misuse of "microbiome." I often now read the expression "members of the gut microbiome," which simply means: gut microbes!

  2. http://lhncbc.nlm.nih.gov/lhc/docs/published/2001/pub2001047.pdf


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