bioinformatics, genomes, biology etc. "I don't mean to sound angry and cynical, but I am, so that's how it comes across"

You’re probably not doing metagenomics

Just to begin, I’d like to say that I’m right about this, and if you think I am wrong, I’m not – you are.

The genome of an organism is the entire complement of genes within an organism’s cells, and genomics is therefore the study of entire genomes.  Metagenomics refers to the study of all genomes within a particular ecosystem, or group of individuals.  Metagenomics therefore refers to studies where entire genomes are assayed.

If you are sequencing a subset of genes (a “barcode”) or a reporter gene such as 16S or 18S, then you’re not doing metagenomics.  You’re just not.  Stop objecting, you’re wrong.  You are not assaying, or attempting to assay, entire genomes, therefore it is incorrect to refer to your study as metagenomics.  I don’t care that 100s of scientists frequently refer to these studies as “metagenomics” in papers and talks; they’re all wrong.

Here are some correct alternatives:

  • Metabarcoding
  • Metagenetics (genetics being the study of genes)

That is all 🙂


  1. Thanks Jonathan, I should have referenced your post!

    I was “inspired” by the some of the “metagenomics” talks at #PAGXXII being anything but….

  2. You are right, AND, I am doing metagenomics. 🙂

  3. Always a step ahead of everyone Jonathan 😉

  4. 16S is metagenomics only for marketing purposes.

  5. Couldn’t agree more. I’ ve been preaching that for years and besides I find 16s sequencing an obsolete approach except in very limited cases. The waste of time and funding that goes into it!

  6. I’m glad I came across this post, even if a bit late. Now I don’t have to write that paragraph in decision letters or reviews; I’ll just post your link 🙂

  7. Words are defined by their usage. You may be right, but if you’re the only one, then you’re wrong no matter how right you may be. Awful isn’t it?

  8. Still, metagenomics is a random, or pseudo-random sampling of genomic material. You typically only get a small fraction of the genomic material that is in the population you are sampling. so metagenomics is not the sequencing of whole genomes, but the sampling of genomic material. I realize that you are differentiating between random and targeted sampling, but neithre are genomics in the sense that you are getting a full genomic information that allows you to do the types of analyses done with whole genomes.

  9. Meta means after or beyond. So neither are “meta”-genomics.

  10. Since we’re quibbling over semantics. Can we stop calling all of the data about the samples that isn’t sequence data “metadata”? Metadata is a term that has been used in many many fields for decades, it is information describing how the data were generated or collected. The salinity of the body of water that you sampled is “data”, the meter that you used to measure salinity is “metadata”.

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