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

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

	FD	DTT	CsCl	MG
Average % read abundance
Mouse	14.26	10.49	1.20	34.63
Phage^a	82.57	86.79	96.13	3.62
Bacteria^b	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 MG^c	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 MG^c	99.998	99.998	99.998	0.00

^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.