Starting with BLASTDB version 5, blastdbcmd has two additional parameters (-taxids and -taxidlists) to efficiently retrieve sequences by taxid.

# Retrieves all human entries; 
# %a prints the accession, %T prints the taxid, %S prints the scientific name
$ blastdbcmd -db nr -taxids 9606 -outfmt “%a %T %S” -target_only 

Note: -target_only is used to ensure that only accessions for the human entries are present. Otherwise, it will present all accessions on any sequence with at least one human sequence. This is important since nr is a non-redundant database.