Is the MDP module sufficient for performing shotgun metagenomic sequencing analyses? I know this module says 16s but seems it is good also for shotgun metagenomics since it seems the Shotgun module is only for functional profiling. I cannot access your protocol publication because I do not have access to Nature. My taxonomic files are abundance files as CSV.
Shotgun metagenomics can generate both gene abundance and taxonomy abundance table (similar to 16s gene). You can take a look at our documentation here.