And this has been covered in the press a bit here and there including
- Spit happens: Saliva's mysteries revealed
- Researchers Find a Unique Bacterial Ecosystem—In Your Mouth
- Study of spit offers insight into human health
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 (
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.
How about microbiomics?ReplyDelete
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).ReplyDelete
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!