Skip to main content

Table 1 Method overview/summary

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

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 throughputa 15-20 15-20 6-8d 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
  1. 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.