The vocabulary used to describe microbial communities: microflora vs microbiota

There has been an explosion of studies that describe microbial communities, mostly spurred by project like the Human Microbiome Project and the democratization of performing high-throughput sequencing. My weekly search for such studies now reveals close to 100 original papers and reviews! This is a good thing as we getting a much better understanding of the role of microbes that live with us and around us. However, this has been accompanied by a ever growing confusion of the terminology associated with describing microbial communities. A recent blog post by Jonathan Eisen highlights one misuse of the word "metagenomics" in the context of marker gene survey, such as 16S rRNA gene sequence-based microbial census. I would like to try to stimulate a conversation to standardize the vocabulary used to describe microbial communities in the scientific literature, and over the next few week, I will write a series of posts dealing with the vocabulary used to describe microbial communities.

I would like to start with one of my pet-peeve, the use of the word "microflora". I fully understand that the word has been used for a long time in the scientific literature, but looking at its definition in all major dictionaries, I feel it is inappropriate to describe any community of microbes.

mi·cro·flo·ra /ˌmīkrōˈflôrə/ noun
1. microscopic plants.
2. the plants or flora of a microhabitat.
origin: 1900–05; micro- + flora

How do these dictionaries define "flora"?
flo·ra [flawr-uh, flohr-uh] noun, plural flo·ras, flo·rae [flawr-ee, flohr-ee]
1. the plants of a particular region or period, listed by species and considered as a whole.
2. a work systematically describing such plants.
3. plants, as distinguished from fauna.
origin: 1655–65; < Neo-Latin, Latin Flōra the Roman goddess of flowers (used from the 17th cent. in the titles of botanical works), derivative of Latin flōr- (stem of flōs ) flower

It is obvious from these definitions and the origins of both words that microflora refers to plants not bacteria. While some dictionaries will include a third definition for microflora that refer to "the aggregate of bacteria, fungi, and other microorganisms normally occurring on or in the bodies of humans and other animals: intestinal flora", this add-on to the definition is the result of over one century of constant misuse of the word driven by a limited understanding of microbes. Our knowledge of microbial communities is now such that we should know better than continuing misusing the word in the scientific literature. I, for one, have contributed to its misuse, as my first grant on human associated microbial communities used the word microflora! Thus, I suggest that to describes the assemblage of microbes living in a microhabitat we use a different term, the word "microbiota", as it is much more encompassing than microflora.

mi·cro·biota [mi″kro-bi-o´tah] noun
1. the microscopic living organisms of a region.
2. the microscopic flora and fauna of a region

Microflora has still its place in the popular literature or in a yogurt advertisement, but microflora does not have its place in the scientific literature anymore.
Let's all stop using the words microflora or flora in scientific papers, conference proceedings, and whenever we can let's educate others. The word microbiota is adequate and appropriate to describe the composition and abundance of microbial communities whether they inhabit the human body or the environment.