You have a list of ids and gis, am I right?
Save the list to the text-file, 16s-sRNAs.txt, each id in a new line,
Go to Batch Entrez:
Read the text on the page, it’s important.
1) select a correct nucleotide database in the upper left corner of the page.
The text on the page explains the difference.
2) select your File in the middle of the menu - 16s-sRNAs.txt from your computer.
3) go to Retrieve - right side of the manu.
In some time you will see what nucleotide sequences NCBI has for this list of IDs.
You can make a database out of the sequences with makeblastdb.
See the following papers, if you need additional information:
The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses.
http://www.ncbi.nlm.nih.gov/pubmed/23460914 , 2013
Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories.
16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2045242/ , 2007