Metaphlan unclassified output

Microbial community profiling MetaPhlAn
1

Dear developers and users,

I have doubts interpreting the metaphlan results. I obtained annotations with the following structure:

k__Bacteria|p__Bacteria_unclassified|c__Bacteria_unclassified|o__Bacteria_unclassified|f__Bacteria_unclassified|g__GGB79097.

Where all taxonomic levels are unclassified except the Kingdom (i.e. they are bacteria) and the last taxonomic level (in this example we know the genus but the family, order, etc. remain unclassified).

Could you help me to understand how to interpret these annotations? How can we know the genus information but not the rest of the taxa?

Thank you very much in advance,

Irene

2

Hi Irene,
this problem derives from the sometimes not informative taxonomy labels in NCBI. In the metaphlan output you can look at the second column (NCBI_tax_id) and search it in the NCBI taxonomy database ( Home - Taxonomy - NCBI ) to get information about the taxonomic levels for the given taxon.

3

Thanks for the reply!