Example of creating a bowtie2-index based on E. coli reference genomes.
# Merge all E. coli reference genomes into one genomes.fna file
cat ref_genomes/ecoli/*.fna > genomes.fna
# create bowtie2 index database (database name: ecoli)
bowtie2-build genomes.fna ecoli
# result: 6 .bt2 database files
ls
ecoli.1.bt2
ecoli.2.bt2
ecoli.3.bt2
ecoli.4.bt2
ecoli.rev.1.bt2
ecoli.rev.2.bt2
# use 'inspect' to check the content of your database
bowtie2-inspect -n ecoli
# define your BOWTIE2_INDEXES directory and move the database files into it
export BOWTIE2_INDEXES=/path/to/my/bowtie2/databases/
cp *.bt2 $BOWTIE2_INDEXES
# bowtie2 mapping: database is defined by option -x
bowtie2 -x ecoli ...
http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#the-bowtie2-build-indexer