Evaluation of the impact of six different DNA extraction methods for the representation of the microbial community associated with human chronic wound infections using a gel-based DNA profiling method

Dilhari, Ayomi; Sampath, Asanga; Gunasekara, Chinthika; Fernando, Neluka; Weerasekara, Deepaka; Sissons, Chris; McBain, Andrew; Weerasekera, Manjula

doi:10.1186/s13568-017-0477-z

AMB Express

Table 2 DNA quality and average DNA yield obtained using different DNA extraction methods

From: Evaluation of the impact of six different DNA extraction methods for the representation of the microbial community associated with human chronic wound infections using a gel-based DNA profiling method

	Patient/specimen No.
	01	02	03	04	05	06	07	08	09	10
1 STES buffer and phenol chloroform extraction method (BP1)
DNA yield (ng/µl)	48.65 ± 25.24	1747.95 ± 404.25	480.2 ± 359.07	195.25 ± 29.06	93.20 ± 31.25	937.75 ± 255.90	900.30 ± 639.79	1096.9 ± 451.7	226 ± 83.43	69.50 ± 10.89
A_260/280	1.98 ± 0.08	1.80 ± 0.01	1.82 ± 0.06	1.88 ± 0.00	1.99 ± 0.02	1.88 ± 0.01	1.80 ± 0.01	1.82 ± 0.01	1.83 ± 0.02	1.96 ± 0.02
A_260/230	0.87 ± 0.05	2.19 ± 0.07	1.75 ± 0.35	1.27 ± 0.02	1.05 ± 0.27	2.15 ± 0.01	1.82 ± 0.40	2.1 ± 0.11	1.69 ± 0.04	0.77 ± 0.05
2 TN150 buffer and phenol chloroform extraction method (BP2)
DNA yield (ng/µl)	10.9 ± 1.56	310.05 ± 160.16	340.6 ± 12.45	88.35 ± 27.51	46.20 ± 21.64	274.05 ± 43.20	661.45 ± 500.70	402.25 ± 1.91	90.25 ± 76.44	93.70 ± 42.99
A_260/280	2.07 ± 0.04	1.8 ± 0.03	1.77 ± 0.00	1.77 ± 0.04	1.73 ± 0.15	1.71 ± 0.02	1.86 ± 0.99	1.82 ± 0.01	1.8 ± 0.06	1.84 ± 0.12
A_260/230	0.52 ± 0.01	1.84 ± 0.16	1.49 ± 0.10	1.15 ± 0.30	0.69 ± 0.17	1.57 ± 0.08	1.66 ± 0.32	1.79 ± 0.08	1.3 ± 0.44	1.37 ± 0.36
3 DNeasy blood and tissue kit (K)
DNA yield (ng/µl)	39.45 ± 21.01	400.55 ± 447.25	698.2 ± 126.99	51.8 ± 28.56	50.75 ± 66.39	152.65 ± 13.08	718.1 ± 608.54	80.95 ± 0.49	316.25 ± 127.77	388.40 ± 120.49
A_260/280	1.87 ± 0.05	1.80 ± 0.01	1.81 ± 0.01	1.78 ± 0.11	1.87 ± 0.17	1.80 ± 0.01	1.82 ± 0.01	1.8 ± 0.01	1.81 ± 0	1.84 ± 0.01
A_260/230	2.1 ± 0.40	1.74 ± 0.66	2.17 ± 0.11	2.19 ± 0.06	1.56 ± 0.00	1.65 ± 0.37	2.15 ± 0.07	1.81 ± 0.11	1.82 ± 0.55	2.15 ± 0.06
4 Heating in distilled water (H1)
DNA yield (ng/µl)	213.25 ± 46.46	51.65 ± 19.02	260.95 ± 70.36	72.2 ± 36.63	142.45 ± 47.73	277.6 ± 9.76	429.05 ± 4.60	145.6 ± 168.57	97.25 ± 73.89	255.35 ± 109.95
A_260/280	1.22 ± 0.04	1.38 ± 0.06	1.26 ± 0.01	1.56 ± 0.05	1.36 ± 0.17	1.39 ± 0.05	1.41 ± 0.05	1.39 ± 0.05	1.41 ± 0.09	1.74 ± 0.18
A_260/230	0.3 ± 0.04	0.28 ± 0.02	0.43 ± 0.00	0.56 ± 0.07	0.29 ± 0.02	0.32 ± 0.01	0.56 ± 1.01	0.33 ± 0.11	0.25 ± 0.04	0.71 ± 0.36
5 Heating in aqueous NaOH (H2)
DNA yield (ng/µl)	131 ± 25.74	356.9 ± 189.22	606.95 ± 82.94	185.5 ± 32.81	146.8 ± 40.45	386.15 ± 96.1	184.25 ± 70.22	240.65 ± 189.86	210.05 ± 28.5	208.6 ± 113.14
A_260/280	1.08 ± 0.04	1.37 ± 0.04	1.51 ± 0.08	1.38 ± 0.05	1.15 ± 0.04	1.31 ± 0.08	1.46 ± 0.02	1.18 ± 0.13	1.1 ± 0.01	1.47 ± 0.03
A_260/230	0.25 ± 0.03	0.46 ± 0.04	0.79 ± 0.13	0.48 ± 0.06	0.26 ± 0.07	0.27 ± 0.02	0.57 ± 0.00	0.25 ± 0.08	0.3 ± 0.02	0.39 ± 0.01
6 Salting out method (S)
DNA yield (ng/µl)	62.2 ± 26.87	1701.8 ± 1046.80	3599.4 ± 1363.87	327.5 ± 286.38	118.45 ± 23.83	581 ± 50.91	3264.4 ± 3135.45	1169.75 ± 582.16	246.85 ± 24.96	1248.4 ± 792.67
A_260/280	1.95 ± 0.04	1.81 ± 0.07	1.81 ± 0.04	1.97 ± 0.13	1.95 ± 0.16	1.78 ± 0.04	1.84 ± 0.06	1.83 ± 0.4	1.83 ± 0.04	1.83 ± 0.11
A_260/230	0.9 ± 0.51	0.61 ± 0.3	0.96 ± 0.01	0.37 ± 0.41	0.15 ± 0.04	0.68 ± 0.03	0.77 ± 0.40	0.48 ± 0.25	0.58 ± 0.11	0.46 ± 0.29

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