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

BMC Genomics

Table 1 Method overview/summary

	FD	DTT	CsCl	MG
Purification steps	Filtration + DNase	DTT + Filtration + DNase	Filtration + DNase + CsCl centrifugation	Total metagenome of unpurified sample
DNA recovered in (ng in sample 1, ng in sample 2)	42, 44	29, 34	21, 19	636, 459
Sample throughput^a	15-20	15-20	6-8^d	N/A
Total duration of protocol (days)^b	1	1	2	N/A
Hands on time (hours)^c	6	6	10	N/A
Special equipment needed	No	No	Ultracentrifuge	N/A
Intra-method reproducibility	High	High	Medium	N/A
Biases against specific phage	Weak	Weak	Strong	N/A
Removal efficiency of mouse DNA	High	High	Very high	N/A
Removal efficiency of bacterial DNA	Very high	Very high	Very high	N/A

^a:Number of samples that can be processed by one person in parallel; ^b:Duration of the respective purification protocol from fecal sample to purified VLPs, DNA extraction time not included; ^c:Hands on time needed for the number of samples that can be processed by one person in parallel (above); ^d:Sample number limited by rotor size of ultracentrifuge and number of density gradients that can be set up in parallel in a reasonable amount of time.

ISSN: 1471-2164