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

In this study we used an in vitro assembled microbiota sample to evaluate the efficiency and biases of purification methods used to purify virus-like particles from gut content for metagenome sequencing. The artificial microbiome sample contained six bacteriophages (P22, phiVPE25, phi6, T3, T7 and M13)two bacterial strains (gr+: Listeria monocytogenes EGD-e and gr-: Bacteroides thetaiotaomicron VPI5482), which were mixed into feces from germ-free mice. Three purification methods were tested: (1) Filtration + DNase (FD), (2) DTT treatment + filtration + DNase (DTT), (3) filtration + DNase + CsCl density gradient (CsCl). Additionally, metagenomes of the complete microbiome sample were sequenced (MG). Each treatment was done in duplicate.