We created Kreken2 + braken databases for CMMG and the Unified human gastrointestinal genome collection (UHGG) with a manually curated taxonomy. They are availalb at https://ezmeta.unige.ch/CMMG/Kraken2db/
We reccomend to use our snakemake pipeline for efficient use of Kraken2 + Braken https://github.com/SilasK/Kraken
Once you have the Kraken2 quantification you can use this jupyter notebook that shows how CMMG can be used for the functional and taxonomic analysis of mouse metagenome data.
The same code can be used for the analysis of human metagenome data, by using our functionally annotions of UHHG.