STC Poll #1 – The De­f­i­n­i­tion of the "Mi­cro­biome"

Great idea, Elio...
But then I won­der: what does "mi­cro­biota" mean?
My spin is that "mi­cro­biota" refers to the or­gan­isms, and "mi­cro­biome" to their many genomes. Jon Eisen is al­ler­gic to the "omics" trend in many ways, but I think it has be­come part of our sci­en­tific lex­i­con.
In­ter­est­ing to see what hap­pens.

All the species at a site: mi­cro­biota
All the genomes at a site: metagenome
Mi­cro­biome isn't an omics word at all, it's an ecol­ogy word — small biome (which would prob­a­bly mean that @phylogenomics would have no prob­lem with it at all, not bad omics). Nei­ther of the above two de­f­i­n­i­tions re­fer to a biome, which re­quires some men­tion of in­ter­ac­tion of the bi­otic with the en­vi­ron­ment.

I agree with Mike Cox, who wrote:
"I ques­tion that we have to make this dis­crim­i­na­tion. The ma­jor­ity of the novel "species" has been de­tected by metage­nomic stud­ies and few of them ac­tu­ally cul­ti­vated. Thus they are known to us by their genomes — and their phys­i­o­log­i­cal prop­er­ties de­duced via e.g. bioin­for­matic path­way re­con­struc­tions."
If the orig­i­nally-de­fined mi­cro­biome can be eas­ily pre­dicted from the 16S taxa, as stun­ningly ev­i­dent in PI­CURSt, then I fail to see the need to dis­tin­guish be­tween mi­cro­biota and mi­cro­biome. The lat­ter is so uni­ver­sally used and rec­og­nized by the pub­lic, it is the place to start and end this de­bate.
Go with mi­cro­biome to cap­ture any metage­nomic study of mi­cro­bial com­mu­ni­ties.

I don't see the dif­fer­ence be­tween "the to­tal­ity of genomes at a site" and "the to­tal­ity of mi­cro­bial species (what­ever that means) at a site." Aren't the species at a given site de­ter­mined by the pres­ence of their genomes? I also agree that the mi­cro­biota are the in­hab­i­tants of a mi­cro-biome, with mi­cro­biome be­ing an eco­log­i­cal term, es­pe­cially in the con­text of a larger or­gan­ism, ie the mi­cro­biome of the hu­man gut im­plies the ecol­ogy of the gut and the host-mi­crobe and mi­crobe-mi­crobe in­ter­ac­tions in the gut.

There are al­ready es­tab­lished eco­log­i­cal terms for these things, so mol­e­c­u­lar bi­ol­o­gists do not need to make up new ones. Biome clearly refers to the ecosys­tem, not just the or­gan­isms. So I voted for Other. The to­tal­ity of the species at a site should be called the Com­mu­nity. The to­tal of the community's genomes would be the metagenome. As with many terms, con­text is im­por­tant, es­pe­cially defin­ing the scale at which you are mea­sur­ing. An ecosys­tem can be tiny or huge.

I think some peo­ple here are mak­ing a lot con­fu­sion with terms.
"Mi­cro­biota" means sim­ply "mi­croor­gan­isms". If it is ap­plied to a spe­cific habitat/space/whatever then we can re­fer to the to­tal­ity of mi­croor­gan­ims in that place as the "mi­cro­biome" of that place. The "place" can be what­ever scale you want to re­fer to, from a small pond to an en­tire planet. Thus, "mi­cro­biome" refers to the to­tal­ity of mi­cro­bial taxa of a cer­tain lo­ca­tion. So yes, you can per­fectly re­fer to the mi­cro­biome of the Baltic Sea.
"Metagenome" and "Metage­nomics" are two dif­fer­ent things, al­though they are re­lated. A "Metagenome" is the to­tal­ity of genomes/genes at a par­tic­u­lar place. "Metage­nomics" is a col­lec­tion of tech­niques to ob­tain in­for­ma­tion about metagenomes.
So, to an­swer Elio's ques­tion, who­ever is us­ing the term "Mi­cro­biome" to de­note all mi­cro­bial genomes at a par­tic­u­lar site is do­ing it wrong. In fact, I work in Metage­nomics and I never came across such a de­f­i­n­i­tion.

Here are my de­f­i­n­i­tions:
Mi­cro­biota: The as­sem­blage of mi­croor­gan­isms present in a de­fined en­vi­ron­ment. i.e. a cen­sus of mi­croor­gan­isms (bac­te­ria, ar­chaea or lower eu­kary­otes...).
Metagenome: The col­lec­tion of genomes and genes from the mem­bers of a mi­cro­biota.
Mi­cro­biome: This term refers to the en­tire habi­tat, in­clud­ing the mi­croor­gan­isms, their genomes (i.e., genes) and the sur­round­ing en­vi­ron­men­tal con­di­tions. This de­f­i­n­i­tion is based on that of "biome", the bi­otic and abi­otic fac­tors of a given en­vi­ron­ments.
Also, let's stop re­fer­ring 16S rRNA gene sur­veys as metage­nomic stud­ies!
See my post at: http://www.allthingsgenomics.com/blog/2013/1/11/the-vocabulary-used-to-describe-microbial-communities-microbiome-metagenome-microbiota

I agree with Jacques Ravel, al­though I have a mi­nor dis­agree­ment, so to speek:
"""Mi­cro­biome: This term refers to the en­tire habi­tat, in­clud­ing the mi­croor­gan­isms, their genomes (i.e., genes) and the sur­round­ing en­vi­ron­men­tal con­di­tions. This de­f­i­n­i­tion is based on that of "biome", the bi­otic and abi­otic fac­tors of a given en­vi­ron­ments."""
I think in­clud­ing genomes/genes in the de­f­i­n­i­tion of "mi­cro­biome" is prob­a­bly not war­ranted. As Jacques says, "mi­cro­biome" is a spe­cial case of the term "biome" used in Ecol­ogy. How­ever, tra­di­tion­aly that term doesn't in­cluded any ref­er­ence to ge­netic ma­te­r­ial present at a "biome". In my opin­ion, nei­ther should it have such a ref­er­ence when refer­ing to "mi­cro­bio­mes". I un­der­stand that much in mi­cro­bi­ol­ogy by ne­ces­sity will have a greater fo­cus on the metabolic/biochemical po­ten­tial of mi­croor­gan­ims, but ge­net­ics should be left out of the de­f­i­n­i­tion of mi­cro­biome. When one refers to the, say, African Sa­vanna biome, one does not in­clude in the de­f­i­n­i­tion the genomes of li­ons or ele­phants, and nei­ther should we do so when refer­ing to mi­cro­bio­mes, even if in prac­tice we need to study that ge­netic po­ten­tial when analysing the func­tions and roles of the mi­croor­gan­isms.