Selective Enrichment and Analysis of Microbial DNA from Contaminating Vertebrate host DNA
Libraries for SOLiD 4 and Ion Torrent PGM sequencing were prepared using NEBNext* Fast DNA Library Prep Set (NEB #E6270) with adaptors and primers compatible with their corresponding platform.  Briefly, genomic DNA was sheared to an average size of 200 bp using the Covaris S2.  Sheared DNA was end repaired, ligated to adaptors, and size selected to an average size of 220-240 bp using E-Gels* (Invitrogen) or Ampure XP beads (Agencourt Bioscience) prior to nick translation and amplification.  Sequencing templates were prepared on the SOLiD EZ Bead (Life Technologies).  50 bp sequencing was performed on the SOLiD 4 Platform (Life Technologies). Similarly, sequencing templates were prepared on the Ion One Touch using the Ion One Touch System Template Kit (Life Technologies).  100 bp sequencing was performed on the Ion Torrent PGM using 316 chips (Life Technologies).