Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”

Microbiome

Table 1 Relative quantification of organisms in the ZymoBIOMICS sample

Species	Genomic 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 proxy	Signature quantitation TSMs^§	Relative biomass contributions—phylopeptidomics signature at species level
Pseudomonas aeruginosa	12	6.58	6.50%	0.49	3.19%	271.3	1.9%
Escherichia coli	12	5.17	8.27%	0.65	5.37%	884.9	6.4%
Salmonella enterica	12	4.78	8.95%	0.96	8.61%	670.2	4.8%
Lactobacillus fermentum	12	1.99	21.49%	1.41	30.38%	3373	24.2%
Enterococcus faecalis	12	3.03	14.11%	0.52	7.39%	1002.8	7.2%
Staphylococcus aureus	12	2.85	15.01%	0.90	13.51%	2380.7	17.1%
Listeria monocytogenes	12	2.98	14.35%	0.27	3.85%	1163.2	8.4%
Bacillus subtilis	12	4.13	10.36%	2.69	27.90%	2946.1	21.2%
Saccharomyces cerevisiae	2	12.13	0.59%	33.51	19.69%	959.7	6.9%
Cryptococcus neoformans	2	19.05	0.37%	33.51	12.54%	267.9	1.9%

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
^§TSM taxon-to-spectrum matches

ISSN: 2049-2618