Since posting the follow up question I’ve done more digging and found this post where you recommended using the -t rel_ab_w_read_stats parameter to obtain species abundances. I ran MetaPhlAn using this parameter on one of our samples and found it had the same species outputted as the default MetaPhlAn run. So this seems to be the preferred parameter to obtain species abundances while also performing the default MetaPhlAn filtering. Is this correct?