Schematic diagram of VLP purification methods. An artificial intestinal microbiota sample was generated by the addition of six phages and two bacterial strains to germ-free mouse feces. Upon homogenization of the mixture, the sample was split into 10 equal subsamples. Two subsamples were immediately set aside for total DNA isolation (metagenome). The remaining 8 samples were centrifuged. Upon completion of centrifugation, two samples were treated with 6.5 mM dithiothreitol (DTT). All eight samples were filtered to remove bacteria and particulates and treated with DNase. Two samples were loaded onto a CsCl gradient and phages were banded as described in Methods. The PEG precipitation failed due to the formation of a viscous mass that impaired PEG removal by buffer exchange. After collection of the phages from the CsCl gradients, all 8 samples were extracted for total nucleic acids using phenol/chloroform extraction. G+, Gram-positive; G-, Gram-negative.