You don't use bwa to run against multiple genomes at once, but you could of course manually align your sequencing data to multiple genomes 1 by 1 using bwa mem or minimap2. Furthermore, for actual metagenome alignment tools, I would look at this paper:
As your question is more complicated than a simple yes or no. To do what you are asking properly there are several things to take into account (which are all discussed in this review).
You will want to look at the readQC metrics as well as the metagenome alignment section (and maybe even metagenome assembly).