TABLE 2

Abundances of Staphylococcaceae species in 46 human nasal specimens, analyzed by rpoB-based conventional and PMA microbiome methods

Detection methodPMA pretreatmentTargetTaxon (at species level)Avg relative abundanceSDRangeNo. (%) of carrying individualsa
Conventional microbiomeNoTotal DNAStaphylococcus epidermidis0.7144840.2542440.078705–0.99235046 (100)
Staphylococcus capitis0.0326340.0766200.000007–0.47912845 (97.8)
Staphylococcus hominis0.0151870.0330890.000002–0.18912343 (93.4)
Staphylococcus aureus0.1224710.1967760–0.65854239 (84.8)
Staphylococcus warneri0.0015620.0039290–0.02046634 (73.9)
Staphylococcus lugdunensis0.0151540.0456350–0.22822025 (54.3)
Staphylococcus haemolyticus0.0016130.0079080–0.05376022 (47.8)
Staphylococcus pasteuri0.0007860.0023830–0.01488822 (47.8)
Staphylococcus caprae0.0020010.0081560–0.05047819 (41.3)
Staphylococcus cohnii0.0003440.0010920–0.00611518 (39.1)
Staphylococcus saprophyticus0.0001840.0005830–0.00351611 (23.9)
Staphylococcus pettenkoferi0.0001690.0007320–0.0037128 (17.4)
PMA microbiomeYesDNA from viable cellsStaphylococcus epidermidis0.7463620.2469510.114632–0.99525046 (100)
Staphylococcus capitis0.0322720.0781190–0.44357040 (86.9)
Staphylococcus hominis0.0141980.0494330–0.29462024 (52.1)
Staphylococcus aureus0.1141280.1935220–0.74036832 (69.5)
Staphylococcus warneri0.0005800.0019210–0.01209318 (39.1)
Staphylococcus lugdunensis0.0132730.0457490–0.25685516 (34.7)
Staphylococcus haemolyticus0.0018090.0119670–0.0811906 (13.0)
Staphylococcus pasteuri0.0009010.0054440–0.0368795 (10.8)
Staphylococcus caprae0.0008480.0049440–0.0333043 (6.5)
Staphylococcus cohnii0.0003730.0023850–0.0161733 (6.5)
Staphylococcus saprophyticus0.0000590.0003500–0.0023542 (4.3)
Staphylococcus pettenkoferi0.0001530.0008740–0.0058342 (4.3)
  • a >1e−5 of relative abundance was defined as the threshold for a positive decision.