Fig. 3
From: Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”
Fit of phylopeptidomics signatures for two experimental proteomic datasets. MS/MS datasets were acquired on a pure Shigella flexneri sample (a), and a 1:1 S. flexneri:Salmonella bongori mixture (b). Instead of the phylogenetic distances for 191 organisms as available in Ciccarelli et al. [20], the distances used here are calculated as detailed in the “Methods” section for 14,237 taxa. The phylogenetic distance from taxon S. flexneri 2a str. 301 is plotted on the x-axis and is calculated as detailed in the “Results” section. The phylopeptidomics signature of a single organism REF is:\( {y}_{i, REF}={N}_{REF1}\times \left({A}_{REF}\times \kern0.45em {e}^{-\frac{x_{i, REF}}{a_{REF}}}+\left(1-{A}_{REF}\right)\times \kern0.33em {e}^{-^{-\frac{x_{i, REF}}{b_{REF}}}}\right) \)with i any taxon, yi, REF the number of TSMs of taxon i due to organism REF, xi, REF the phylogenetic distance between i and REF, aREF and bREF coefficients for the two exponential terms, AREF a repartition term, and NREF the term indicating the quantity of organism REF. a Sample L00221 from Supplementary Table SI, corresponding to a 1:0 Shigella:Salmonella ratio. The display is along xi, REF1 x-axis with REF1 = S. flexneri 2a str. 301, REF2 = S. bongori NCTC 12419, NREF1 = 2697 and NREF2 = 21 as fitted. The S. flexneri 2a str. 301 signature is displayed in a blue filled area. b Sample L00306 from Supplementary Table SI, corresponding to a 1:1 Shigella:Salmonella ratio. The display is along xi, REF1 x-axis with REF1 = S. flexneri 2a str. 301, REF2 = S. bongori NCTC 12419, NREF1 = 1492, and NREF2 = 1558 as fitted. The S. flexneri 2a str. 301 and S. bongori NCTC 12419 signatures are displayed respectively in blue- and orange-filled areas. The relative percentage of S. flexneri calculated using phylopeptidomics signatures is thus 1492/3050 = 49% compared with 50% expected