6 Comments

The Re­sult of the Mi­cro­biome Poll

The re­sults from 135 votes are:

What have we learned?

  • The var­i­ous com­ments con­firm that the term mi­cro­biome means dif­fer­ent things to dif­fer­ent peo­ple.
  • Lita points out that in the early days when HMP was 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." It seems that they did not dis­tin­guish be­tween op­tion A and B but fused them to­gether.
  • Sev­eral com­menters pro­pose that the term refers to the whole ecosys­tem, not just the or­gan­isms. (Vicky, Pe­dro, Jacques). Biome alone means ecosys­tem but Rob points out that it de­pends on whether you parse mi­cro­biome "mi­cro-biome" or "mi­crobi-ome." The lat­ter may sug­gest that it's an­other "-ome, sensu genome, tran­scrip­tome, etc. 
  • Some pre­fer metagenome for op­tion B (Mike, Pe­dro). Jonathan points out that it refers to non-mi­cro­bial cases as well.
  • Some sug­gest that there is no need to dif­fer­en­ti­ate be­tween op­tions A and B (Christoph, Sponch) be­cause most mi­crobes have not been cul­ti­vated and are known from their genome. Ergo, their genome IS the or­gan­ism.
  • In keep­ing with the con­fu­sion, there is dis­agree­ment about whether mi­cro­biome and mi­cro­biota are syn­ony­mous.

In con­clu­sion

The num­bers in­di­cate that there is no con­sen­sus about the us­age of the term mi­cro­biome.  Op­tion A gets more votes, but not by a huge fac­tor. Thus, vox pop­uli did not re­solve the ques­tion. It re­mains open.

 

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6 Comments
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bks
12 years ago

I think op­tion 'C' is sup­posed to be "Some­thing else" not a re­peat of op­tion 'B'.
–bks
Elio replies: Yes, a mis­take. We'll fix it stat. Many thanks.
Elio

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Nathan Myders
12 years ago

Nathan My­ers writes:
1. It both­ers me to see a biome re­duced to a gene mix. Genes are
cer­tainly im­por­tant, even es­sen­tial, but do not rep­re­sent the
to­tal­ity of any­thing real. To me any de­fen­si­ble de­f­i­n­i­tion of a
biome must take in the com­plete set of in­di­vid­ual or­gan­isms present,
in their po­si­tions and re­la­tion­ships — in­clud­ing cuckoo eggs in
other birds' nests, mi­to­chon­dria in their re­spec­tive hosts, mice
half-di­gested in a fox and con­tribut­ing their mi­crobes to to its
in­testi­nal flora, bac­te­ria in fully-formed films. A mi­cro­biome,
then, sim­ply omits the ex­ces­sively mul­ti­cel­lu­lar eu­kary­otic
par­tic­i­pants. It is de­fined by what it ex­cludes.
Such a de­f­i­n­i­tion evokes Her­a­cli­tus — you can­not tread on the
same biome twice — so we can only speak pre­cisely in the plural,
or over a du­ra­tion, of a fam­ily of re­lated or evolv­ing bio­mes.
But, for just that rea­son, it should of­fer us no new dif­fi­culty.

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Thomas Jové
12 years ago

In French we use an­other name for the to­tal­ity of mi­cro­bial species, that is "mi­cro­biote" while mi­cro­biome refers to the DNA. I sug­gest eng­lish na­tive to get a word too, oth­er­wise we could use the french word "mi­cro­biote" since it "sounds" en­glsih as well

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Thomas Jové
12 years ago

In­stead, our pbm is that in french "mi­cro­biome" also refers to the whole ecosys­tem...

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Bilal Ayub
12 years ago

Sir, the ar­ti­cle is quite in­for­ma­tive. I have learned quite a lot from this. Thank you so much for shar­ing this in­for­ma­tion !!!

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Pedro
12 years ago

"""Biome alone means ecosys­tem but Rob points out that it de­pends on whether you parse mi­cro­biome "mi­cro-biome" or "mi­crobi-ome." The lat­ter may sug­gest that it's an­other "-ome, sensu genome, tran­scrip­tome, etc."""
A late com­ment, but may be use­ful for pos­ter­ity. Al­though Rob did have a point re­gard­ing the pars­ing of the term "Mi­cro­biome", it should be men­tioned that the term was orig­i­naly coined by Leder­berg to mean "the eco­log­i­cal com­mu­nity of com­men­sal, sym­bi­otic, and path­o­genic mi­croor­gan­isms that lit­er­ally share our body space". He was re­fer­ring to the *hu­man* mi­cro­biome, but that's ir­rel­e­vant. The rel­e­vant part is that the term was orig­i­nally con­ceived as be­ing based on the *biome* de­f­i­n­i­tion from Ecol­ogy. There­fore there is no doubt that the term means "all the mi­croor­gan­isms and their en­vi­ron­ment", and not a col­lec­tion of genomes (that is the Metagenome of a Mi­cro­biome).
In my opin­ion, there is a lot of mis­use of the term, and this should by no means be taken as mean­ing that the ques­tion "re­mains open".
Link to lederberg's ar­ti­cle: http://www.the-scientist.com/?articles.view/articleNo/13313/title/-Ome-Sweet–Omics—A‑Genealogical-Treasury-of-Words/
My 2 cents.

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