The microbiome and metagenome, what's the difference?

Depends who you ask.

The microbiome and metagenome, what's the difference?
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One of the things we come across during the development of new fields of science is that sometimes the vocabulary we have to describe the world isn’t sufficient.

When that happens, we need to invent new words (or mash up old words to make new words)!

But because this is science, it means we also spend a lot of time disagreeing on the definitions of words until we reach a consensus on what those words actually mean.

This usually happens once we have enough data to clearly define what it is that we are seeing!

But with respect to the ‘microbiome’ and the ‘metagenome,’ things are still a little murky.

There are two commonly used definitions for the microbiome, one has its roots in genetics and the other in ecology.

The genetics one is a mashup of microbi and ome (still pronounced micro-biome) and it is defined as all of the genomes of microorganisms found in a particular habitat.

The ecology one is a combination of micro and biome, and a biome in ecology describes all of the biotic and abiotic (environmental) factors that are found in a distinct geographic region.

So, a ‘microbiome’ in that version of the definition is just a micro version of a traditional biome.

It’s pretty confusing to have two very different definitions of a word.

But wait!

There’s more, because I haven’t told you about the metagenome yet!

Some people define it identically to the microbiome - it's the genomes of all of the microorganisms found in a particular habitat.

Others define it as all of the genetic information found in a habitat (inclusive of the host and any other environmental DNA from non-microorganisms).

Some say the microbiome is a subset of the metagenome.

Others claim that since the metagenome is just about genetics, it’s actually a subset of the microbiome!

Are you confused yet, because I certainly am!

But don’t worry, even microbiologists find this confusing, and in 2020 a controversial paper was published in the journal ‘Microbiome’ which tried to reconcile the competing definitions of all of these words.

In it the authors define the microbiome as all of the microbiota in a habitat inclusive of the theater of activity, meaning, they combined the two 'microbiome' definitions together.

In the case of microbiomes that occur on or in animals (like humans), this definition lumps them into the ‘theater of activity,’ too.

Which also means this definition eats all definitions of the metagenome because that definition can only be inclusive of 'genomes!'

While the definitions proposed by this paper provide order and logic to these words, we’re still probably decades from consensus on this!


Berg G, et al. 2020. Microbiome definition re-visited: old concepts and new challenges. Microbiome. DOI: 10.1186/s40168-020-00875-0 Premium 27
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