Molecular Biology 101: What’s an -ome when it’s at home?


Genome

Proteome

Transcriptome

Exome

Microbiome?

All of these words are becoming part of the scientific vernacular, and new ones are arising all the time. But is this proliferation of terms meaninful, or even a good thing? 

The first -ome

In its modern molecular biology form, genome was the first of these -omes to be coined, back in 1920 in a book by the name of “Verbreitung und Ursache der Parthenogenesis im Pflanzen- und Tierreiche” by Hans Winkler. (Distribution and causes of parthenogenesis in the plant and animal kingdoms… No that wasn’t an opportunity to point out I speak German. But yes, I am cool like that.) The genome is the sum total of all the genetic information in an organism. When a scientist says she studies genomics, she means that she looks at all of the DNA in an organism, (like how much of it there is, or what order the genes are in) rather than working on a particular gene. -ome can be thought of as a sort of holistic suffix, implying everything within a system.

A holistic approach

So what about the rest of these -omes? They pretty much follow a theme. Proteomics is about comparing the levels of protein production between different species or different groups in an experiment (e.g. which proteins are up-regulated if you grow a plant in freezing conditions?) The transcriptome is all of the genes that are actually transcribed (or copied from DNA into RNA). So while two species of plant may be very similar at the genome level, if one of them expresses a completely different set of those shared genes, its transcriptome may look very different.

More recently, you’ll have been hearing a lot about the microbiome: which is where we study all of the microbes in a particular variety. There’s the Human Microbiome Project, a five year study of the bacterial flora of humans, to allow comparisons between healthy and diseased individuals, with potentially major repercussions for medicine as we know it, which has unfortunately been attracting some major criticism recently. Within that are separate sub projects like the vaginal microbiome and the gut microbiome. There are also plenty of quirky projects like Rob Knight swabbing a captive komodo dragon to see how its microbiome differs from that of dragons in the wild, and the Kitten Microbiome Projectall comparing the micro-organisms found on particular macro-organisms.

How many?! 

Clearly some of these are sensible, helpful, necessary terms. But websites like omics.org list some 250 different kinds of -ome (500 lines of -ome and -omics pairs). Do we really need that many? (My favourite, incidentally, is Antiome: The totality of people who object the propagation of omes.) In fairness, some of plenty of these aren’t actually being used by anyone to describe their field, but at least a hundred really are. There are actually papers using the words foldome and functome and organome, the latter of which I find faintly ridiculous. Jonathan Eisen is responsible for the phylogenomics blog where he keeps a running Badomics” word of the day.

At the end of the day, I don’t think we need all of these terms. But I guess as long as they make a useful distinction for people (like allowing them to search Web of Science more easily!) then the surge in omomics is only likely to continue!

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