Is the 'Actinobacteria bacterium' a species rank taxonomy annotation?

Question

[paradox]

Hi all, I used the diamond and nr database to get the gene taxonomy annotations and found many annotations like ' Actinobacteria bacterium' on species rank . my boss told me that's not a species name , the output is wrong. I got the NCBI tax name by the taxid , that's what the diamond output , any one know something about it?

Answer 1

[andres.firrincieli]

Your boss is right. Actinobacteria bacterium refers to a record classified only at Phylum level by the submitter.

edit: keep in mind that NCBI do not perform any kind of manual curation regarding the taxonomy

[paradox]

This is a big favor, I used to take the NCBI as standard! so, should manually amend the wrong rank annotations? is there any software that can help to do that?

[GenoMax]

nr database is a comprehensive collection of all protein sequences in GenBank. If you need to do more specific identification then you would want to use a curated database like RefSeq genomes.

[andres.firrincieli]

I am sorry but I am not aware of any tool that do these kind of fixes.

ps. I am not saying that you have to do that manually

[paradox]

now I get it, thanks for your help!

Answer 2

[Mensur Dlakic]

Actinobacteria bacterium is not necessarily a wrong annotation - it just isn't very precise. It could very well be that the bacterium belongs to that phylum.

Why didn't the authors do a more detailed classification? Most likely nothing very close at the family/genus/species level was available at the time they submitted the sequences, so the best they could do was assign a phylum. If you backtrack to a genome your proteins belong to, you may be able to find a more informative taxonomic classification in GTDB database, specifically in Actinobacteria:

https://gtdb.ecogenomic.org/tree?r=p__Actinobacteriota

[Mensur Dlakic]

To give you a concrete example:

https://www.ncbi.nlm.nih.gov/assembly/GCA_003599235.1

The NCBI name of this organism is Actinobacteria bacterium (high GC Gram+) which is similar to what you have, and not very informative. If you go to GTDB, a much better classification is provided:

https://gtdb.ecogenomic.org/genomes?gid=GCA_003599235.1

It is classified as:

d__Bacteria; p__Actinobacteriota; c__UBA9087; o__SURF-47; f__SURF-47; g__SURF-47; s__SURF-47 sp003599235

[paradox]

I'm truly grateful for your help, now I get what to do next