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Table 1 Relative quantification of organisms in the ZymoBIOMICS sample

From: Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

SpeciesGenomic DNA composition (%)Genome size (median total length in Mb)Cell count ratio (with 1 genome copy)Estimated cell volume (in μm3)Relative biomass contributions—cell volume proxySignature quantitation TSMs§Relative biomass contributions—phylopeptidomics signature at species level
Pseudomonas aeruginosa126.586.50%0.493.19%271.31.9%
Escherichia coli125.178.27%0.655.37%884.96.4%
Salmonella enterica124.788.95%0.968.61%670.24.8%
Lactobacillus fermentum121.9921.49%1.4130.38%337324.2%
Enterococcus faecalis123.0314.11%0.527.39%1002.87.2%
Staphylococcus aureus122.8515.01%0.9013.51%2380.717.1%
Listeria monocytogenes122.9814.35%0.273.85%1163.28.4%
Bacillus subtilis124.1310.36%2.6927.90%2946.121.2%
Saccharomyces cerevisiae212.130.59%33.5119.69%959.76.9%
Cryptococcus neoformans219.050.37%33.5112.54%267.91.9%
  1. Cell counts were estimated based on one genome copy per cell. Cell volumes were roughly estimated based on the known morphology and dimensions of each species in classical growth conditions. The corresponding ratio of cell volumes is indicated as a possible proxy for biomass contributions assuming that the protein biomass may be correlated to the cell volume. These rough estimations are given only for an overview of possible biomass contributions for the ten species. The phylopeptidomic signature quantitation based on TSMs is indicated for each species as well as the corresponding calculated relative biomass contributions
  2. §TSM taxon-to-spectrum matches