Thread by @ElinVidevall

The word #Microbiome is derived from the word "biome", i.e. a distinct environmental habitat, in which microbes occupy and are part of. A Microbiome is therefore a spatially distinct environment with unique bio-physical properties AND its associated microbes. 🦠+🏝️

#Microbiota refers to the microbial members of the microbiome. 🦠 This word is therefore strongly related to this microbial biome but it does not concern the environmental conditions of the specified habitat.

I see lots of people and papers still defining #microbiome as a "collection of genes/genomes". Worth knowing though is that "microbiome" is not an -omics word related to the word genome. We have another, more appropriate, word to describe a collection of genomes: #metagenome

Marchesi & Ravel outlined the definitions of these terms in 2015. The journal @MicrobiomeJ uses these terms officially. Cited below: microbiomejournal.biomedcentral.com/articles/10.11…

#Microbiome "refers to the entire habitat, including the microorganisms (bacteria, archaea, lower and higher eukaryotes, and viruses), their genomes (i.e., genes), and the surrounding environmental conditions. This definition is based on that of biome,...

...the biotic and abiotic factors of given environments." #Microbiota is defined as "The assemblage of microorganisms present in a defined environment." And #Metagenome as "The collection of genomes and genes from the members of a microbiota. "

Wikipedia claims that the term #Microbiome was first defined in 1988 by Whipps et al. as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. en.wikipedia.org/wiki/Microbiome

Berg et al. outline the history of microbiome research in their recent study.
#Microbiome is here defined as "a characteristic microbial community occupying a reasonable well-defined habitat which has distinct physio-chemical properties" ...

microbiomejournal.biomedcentral.com/articles/10.11…

... "The #microbiome not only refers to the microorganisms involved but also encompass their theatre of activity, which results in the formation of specific ecological niches."

"The #microbiota consists of the assembly of microorganisms belonging to different kingdoms /.../, while “their theatre of activity” includes microbial structures, metabolites, mobile genetic elements.."

Jonathan Eisen @phylogenomics also discussed these terms and the origin of the word #microbiome in a blog post a few years ago. microbe.net/2015/04/08/wha…

Also, seeing how I now started this thread: #Holobiont = an organism and all its associated microbes. #Hologenome refers to the genomes of holobionts, i.e. the host genome + the microbial metagenomes. #Hologenomics