From John Anderson, Ph.D. BioSample curation staff
"We consider any environmental or clinical sample that may contain multiple organisms (usually microbial, including archea, bacteria and fungi but not restricted to those) from which data will be derived, to be a "metagenome". The terminology is partially historical, since the first instances of this sample type were for genomic sequencing, but it now includes any sample of this type, regardless of the type of data that will be taken, so a sample for a transcriptome project or a genome project would get the same taxonomy name. You can think of NCBI "metagenome" taxonomy nodes as meaning "microbiomes".
The "metagenome" taxonomy nodes are under "unclassified sequences", since there is not a specific lineage.
https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=408169
You'll see that these are mostly divided into "ecological metagenomes" and "organismal metagenomes". The names are reflective of the source, not the organisms that will be identified. These are created on an "as needed" basis, so not every imaginable type is present. Current practice is to use an existing node wherever possible."
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