What command/invocation is used to generate NCBI 16SMicrobial blastdb
Running blastdbcmd -db foo -info provides a little information but I haven't seen anything which will report exactly how a blastdb was created.
A blastdb readme suggests that only the parse_seqids option has been added to the standard parameters.

For those from NCBI, the following makeblastdb commands are recommended:

For nucleotide fasta file:   makeblastdb -in input_db -dbtype nucl -parse_seqids
For protein fasta file:      makeblastdb -in input_db -dbtype prot -parse_seqids


The -parse_seqids requires NCBI fasta headers in the correct format (spec can be found here).