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Table 4 Removal efficiency of mouse and bacterial DNA by different purification methods

From: Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

 

FD

DTT

CsCl

MG

Average % read abundance

   

Mouse

14.26

10.49

1.20

34.63

Phagea

82.57

86.79

96.13

3.62

Bacteriab

0.033

0.032

0.032

59.21

Calculations based on average % read abundance

 

Phage/mouse ratio

5.79

8.27

80.31

0.10

Factor of ratio change compared to MG method

55

79

768

1

Estimated % decrease of read generating mouse DNA as compared to MGc

98.19

98.74

99.87

0.00

Phage/bacteria ratio

2537.74

2674.62

2999.83

0.06

Factor of ratio change compared to MG method

41518

43757

49078

1

Estimated % decrease of read generating bacterial DNA as compared to MGc

99.998

99.998

99.998

0.00

  1. a:Sum of read abundances for all added bacteriophage (this excludes the phiX174 used as Illumina internal control); b:Sum of read abundances for the two added bacteria – L. monocytogenes and B. thetaiotaomicron; c:Calculated based on read abundances normalized to phage read abundance.