You can find the current list of baterial genomes available at NCBI here. Since the choice of genomes is somewhat subjective, you may need to decide what combination will work for you.

Isn't ncbi refseq what you are looking for ?

a curated, non-redundant collection of reference sequences

Or maybe you can look into previous consortium effort to get non-redundant DB, such as HMP.


Nb : In case you want to download bacterial refseq, here is the recipe :

# Prepare dir & url
mkdir -p DL_refseq_bacteria && cd $_;
ftp_url='ftp://ftp.ncbi.nlm.nih.gov/refseq/release/bacteria';
# Create list of urls to DL
curl --silent --list-only $ftp_url/* | grep -i 'genomic.fna.gz' > list.txt;
sed -i "s|^|$ftp_url/|" list.txt;
# Actual DL
while read url; do axel -q $url; done < list.txt;
# Clean files
cat *.fna.gz > ncbi_refseq_release_bacteria.fna.gz;
rm -f !(ncbi_refseq_release_bacteria.fna.gz);

Ps : Be aware that this is going to take some time to DL 100+ Go of data

Hi, same issue here, did yo end up finding a way to get this set? thanks