If you find that the word ‘microbiome’ has crept into your lexicon but you don’t really know what it means or how to use it – fear not, you’re not alone. Microbiome is a new-ish term to describe something that has been studied for almost a century: the collection of microorganisms in a dynamic ecosystem, including who they are and what they are doing.
Picture a crowd of humans. Maybe this one:
The picture is just one instant in an event involving hundreds or thousands of organisms that were all doing a lot of different things, sometimes for just a few seconds. How would you describe it?
Maybe using the number of members present in this community? Or a list of names of attendees? The 16S rRNA gene for prokaryotes, or the 18S rRNA or ITS genes for eukaryotes, for examples, would tell us that. Those genes are found in all types of those organisms, and is a pretty effective means of basic identification. But, it’s only as good as how often that gene is found in the organisms you are looking for. There is no one gene that’s found exactly the same in all organisms, so you might need to target multiple different identification genes to look at all the different types of microorganisms, such as bacteria, fungi, protozoa, or archaea. Viruses don’t share a common gene across types, to look at viruses you’d need something else.
From our identification genes we could identify all the organisms wearing yellow; ex. phylogenetic Family = Ducks. That wouldn’t tell us if they were always found in this ecosystem (native Eugene population) or just passing through (transient population), but we could figure that out if we looked at every home game of the season and found certain community members there time and again.
But knowing they are Ducks doesn’t tell us anything else about that community member. What will they do if it starts raining? Are they able to go mountain biking? Perhaps we could identify their potential for activity by looking at the objects they are carrying? That would be akin to metagenomics, identifying all the DNA present from all the organisms, which tells us what genes are present, but not if they are currently or ever used. It can be challenging to interpret: think of sequencing data from one organism’s genome as one 1,000,000-piece puzzle and all the genomes in a community as 1,000 1,000,000-piece puzzles all dumped in a pile. In the crowd, metagenomics would tell us who had a credit card that was specifically used to buy umbrellas, but not whether they’d actually use the umbrella if it rains (ex. Eugeneans would not).
We could describe what everyone is doing at this moment. That would be transcriptomics, identifying all the RNA to determine which genes were actively being transcribed into proteins for use in some cellular function. If we see someone in the crowd using that credit card for an umbrella (DNA), the receipt would be the RNA. RNA is a working copy you make of the DNA to take to another part of the cell and use as a blueprint to make a protein. You don’t want your entire genome moving around, or need it to make one protein, so you make a small piece of RNA that will only hang around for a short period before degrading (i.e. you crumpling that RNA receipt and throwing it away because who keeps receipts anymore).
Using transcriptomics, we’d see you were activating your money to get that umbrella, but we wouldn’t see the umbrella itself. For that, we’d need metabolomics, which uses chemistry and physics instead of genomics, in order to identify chemicals (most often proteins). Think of metabolomics as describing this crowd by all the trash and crumbs and miscellaneous items they left behind. It’s one way to know what biological processes occurred (popcorn consumption and digestion).
From a technical standpoint, researching a microbiome might mean looking at all the DNA from all the organisms present to know who they are and of what they are capable. It might also mean looking at all the RNA present, which would tell you what genes were being used by “everyone” for whatever they were doing at a particular moment. Or you might also add metabolomics to identify all the chemical metabolites, which would be all the end products of what those cells were doing, and which are more stable than RNA so they could give you data about a longer frame of time. Collectively, -omics are technology that looks at all of a certain biological substance to help you understand a dynamic community. However, it’s important to remember that each technology gives a particular view of the community and comes with its own limitations.