Hi @bdpessem
Sorry for the misunderstanding, the metaphlan marker genes were identified from 100k reference genomes and expands 17,000 microbial species. We don’t have an available list of the GCAs used but it can be retrieved following the description of the data retrieval in our last paper: Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 | eLife
Regarding to the species detected, you can get a more sensitive profiling by modifying the --stat_q parameter, please, have a look at this post: Fungal signatures - #2 by aitor.blancomiguez
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