Extend the mOTUs database - motu-tool/mOTUs GitHub Wiki
The mOTUs database is constructed from reference genomes and metagenome assembled genomes (MAGs).
If you reconstruct MAGs from your metagenomic samples, you can add them to the mOTUs database and you can also check to which mOTUs they map to.
The scripts to do this are in https://github.com/motu-tool/mOTUs-extender.