Extended Data Fig. 1: MK-SpikeSeq reliably measures absolute abundances across kingdoms.

a, d, A set of single-kingdom mock communities with a fixed composition of 10 bacterial (a) or 10 fungal (d) species and variable total microbial loads (indicated by the pie chart schematics underneath), were quantified using MK-SpikeSeq for relative composition (coloured bars) and absolute abundance (black or grey bars). b, e, Correlations between expected (based on initial microbial densities and known dilution factors) and MK-SpikeSeq-measured total absolute abundances of bacteria (b) and fungi (e) show that MK-SpikeSeq reliably detects absolute abundances of bacteria and fungi. For e, as exact rDNA copy numbers per fungal cell are undefined, the expected total abundances of internal transcribed spacer 1 (ITS1) are only estimates (here using 200 rDNA copies per fungal cell). c, f, Changes in absolute abundance for individual members (colour-coded as in a, d) of the bacterial (c) and fungal (f) mock communities are largely consistent with known dilution factors. g, A set of serial dilutions of a human faecal sample was quantified using MK-SpikeSeq for relative composition (coloured bars; shown are the phylum-level taxa) and absolute abundance (empty bars). h, Changes in absolute abundance for individual taxa (colour-coded in phyla as in g) across kingdoms are largely consistent with known dilution factors.