Table 3 Comparison of performance between qPCR and ddPCR based on three DNA extraction methods
From: Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples
Method | L. reuteri DSM 17938 spiked (Log10 cells/g) | Phenol–chloroform-based method (PC) | QIAamp Fast DNA Stool Mini Kit-based method (QK) | Protocol Q-based method (PQ) | |||
|---|---|---|---|---|---|---|---|
Mean ± SDb (Log10 cells/g) | CVc (%) | Mean ± SD (Log10 cells/g) | CVc (%) | Mean ± SD (Log10 cells/g) | CVc (%) | ||
qPCR | 7.97 | 7.53 ± 0.12 | 1.58 | 7.62 ± 0.13 | 1.77 | 7.89 ± 0.12 | 1.53 |
6.97 | 6.53 ± 0.17 | 2.59 | 6.63 ± 0.14 | 2.12 | 6.91 ± 0.11 | 1.55 | |
5.97 | 5.61 ± 0.24 | 4.23 | 5.63 ± 0.21 | 3.66 | 5.90 ± 0.04 | 0.60 | |
4.97 | 4.92 ± 0.34 | 6.85 | 4.71 ± 0.16 | 3.44 | 5.04 ± 0.11 | 2.20 | |
4.67 | 4.86 ± 0.30 | 6.17 | 4.46 ± 0.18 | 3.96 | 4.75 ± 0.10 | 2.18 | |
4.37 | - | - | 4.31 ± 0.16 | 3.67 | 4.54 ± 0.14 | 2.98 | |
4.07 | - | - | 4.08 ± 0.23 | 5.61 | 4.28 ± 0.07 | 1.67 | |
3.77 | - | - | 3.95 ± 0.17 | 4.22 | 4.11 ± 0.15 | 3.67 | |
Blanka | 4.72 ± 0.49 | 10.38 | 3.72 ± 0.30 | 8.09 | 3.89 ± 0.15 | 3.81 | |
ddPCR | 7.97 | 7.43 ± 0.04 | 0.59 | 7.80 ± 0.03 | 0.34 | 7.86 ± 0.08 | 1.07 |
6.97 | 6.41 ± 0.07 | 1.03 | 6.72 ± 0.02 | 0.30 | 6.87 ± 0.11 | 1.66 | |
5.97 | 5.40 ± 0.12 | 2.17 | 5.66 ± 0.04 | 0.74 | 5.89 ± 0.11 | 1.79 | |
4.97 | 4.88 ± 0.15 | 3.01 | 4.66 ± 0.05 | 1.10 | 4.85 ± 0.09 | 1.92 | |
4.67 | 4.76 ± 0.09 | 1.93 | 4.26 ± 0.16 | 3.69 | 4.54 ± 0.05 | 1.17 | |
4.37 | - | - | 4.06 ± 0.05 | 1.25 | 4.29 ± 0.10 | 2.33 | |
4.07 | - | - | 3.74 ± 0.20 | 5.38 | 4.21 ± 0.23 | 5.41 | |
3.77 | - | - | 3.62 ± 0.21 | 5.91 | 3.86 ± 0.20 | 5.28 | |
Blanka | 4.28 ± 0.22 | 5.20 | 3.57 ± 0.19 | 5.34 | 3.66 ± 2.21 | 60.26 | |