Table 6 Colony forming unit-normalized 16S r DNA copy number for the best extraction protocols (Tables 1 , 2 and 3 ) associated with three biological replicates of various Gram-negative Eubacteria (P—S)
From: The near-quantitative sampling of genomic DNA from various food-borne Eubacteria
Copies 16SrRNA “gene” per CFU | |||||||
|---|---|---|---|---|---|---|---|
Gram Neg isolates | Extraction method | Culture 1 | Culture 2 | Culture 3 | Mean | Stdev | |
Pantoea agglomerans | High Pure | 15.7 | 10.8 | 9.97 | 12.2 | 3.10 | a |
Agencourt | 13.2 | 16.2 | 15.2 | 14.9 | 1.53 | ab | |
OmniLyse | 20.8 | 23.3 | 29.8 | 24.6 | 4.65 | b | |
CFU mL−1 | |||||||
5.04 × 108 | 5.03 × 108 | 4.09 × 108 | |||||
±12.4% | ±12.6% | ±10.9% | |||||
Pseudomonas oleovorans | High Pure (TSB) | 38.6 | 30.4 | 24.9 | 31.3 | 6.89 | a |
Agencourt (TSB) | 36.7 | 42.3 | 48.9 | 42.6 | 6.11 | ab | |
OmniLyse (TSB) | 69.9 | 52.4 | 58.1 | 60.1 | 8.93 | ab | |
OmniLyse (LB) | 73.0 | 120 | 205 | 133 | 66.9 | b | |
CFU mL−1 (TSB) | |||||||
5.21 × 107 | 4.62 × 107 | 5.17 × 107 | |||||
±7.10% | ±0.729% | ±7.82% | |||||
(LB) | |||||||
4.89 × 107 | 2.70 × 107 | 1.89 × 107 | |||||
±17.1% | ±4.36% | ±25.8% | |||||
Rahnella aquatilis | High Pure | 5.15 | 5.43 | 6.28 | 5.62 | 0.588 | a |
Agencourt | 7.83 | 8.57 | 7.05 | 7.82 | 0.760 | b | |
OmniLyse | 16.7 | 13.3 | 11.5 | 13.8 | 2.64 | c | |
CFU mL−1 | |||||||
6.04 × 108 | 7.07 × 108 | 8.13 × 108 | |||||
±16.0% | ±13.5% | ±16.1% | |||||
Salmonella Typhi | High Pure | 3.17 | 3.81 | 4.69 | 3.89 | 0.763 | a |
Agencourt | 10.7 | 8.10 | 8.48 | 9.09 | 1.40 | a | |
OmniLyse | 7.50 | 5.71 | 6.39 | 6.53 | 0.904 | ab | |
CFU mL−1 | |||||||
8.98 × 108 | 7.70 × 108 | 7.13 × 108 | |||||
±0.750% | ±3.72% | ±2.60% | |||||
Serratia preteamaculans | High Pure | 3.24 | 3.35 | 6.57 | 4.39 | 1.89 | b |
Agencourt | 5.59 | 5.34 | 6.57 | 5.83 | 0.650 | b | |
OmniLyse | 0.325 | 1.88 | 1.32 | 1.18 | 0.788 | a | |
CFU mL−1 | |||||||
1.33 × 109 | 1.19 × 109 | 1.19 × 109 | |||||
±12.8% | ±11.7% | ±13.4% | |||||