The main description of MetaPhlAn3 (MetaPhlAn4 – The Huttenhower Lab) states:
accurate estimation of organismal relative abundance (in terms of number of cells rather than fraction of reads);
Given that many bacteria and archaea are polyploid (eg., https://jb.asm.org/content/193/3/734.long & Polyploidy in Archaea and Bacteria: About Desiccation Resistance, Giant Cell Size, Long-Term Survival, Enforcement by a Eukaryotic Host and Additional Aspects | Journal of Molecular Microbiology and Biotechnology | Karger Publishers), does MetaPhlAn3 account for ploidy when estimating number of cells (rather than fraction of reads) from marker abundances?