From the bowtie2 manual:

Bowtie 2 can be run on many threads. By default, Bowtie 2 uses the Threading Building Blocks library (TBB) for this. If TBB is not available on your system (e.g. make prints an error like tbb/mutex.h: No such file or directory), you can install it yourself from source (see Threading Building Blocks library) or install it using your operating system's preferred package manager. The table below list some of the commands for a few of the more popular operating systems.

If all fails Bowtie 2 can be built with make NO_TBB=1 to use pthreads or Windows native multithreading instead.

This conda package contains a build of bowtie2 that was compiled with the NO_TBB=1 flag, for users that are not able to install the external dependencies.