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 🙂