fecal metagenome
Genomic DNA libraries were constructed for sequencing on the Illumina platform using the KAPA Library Preparation Kit (Kapa Biosystems, Woburn, MA). First, DNA was fragmented with the Covaris E220( Woburn,MA). Then libraries were prepared using a modified version of manufacturers protocol. The DNA was purified between enzymatic reactions and the size selection of the library was performed with  SPRIselect beads (Beckman Coulter Genomics, Danvers, MA).   Unique Dual indexes of  8 nucleotides in length are added to each sample during a final Library amplification step.  Primer pairs for indexing were purchased from NEB (New England Biolabs, Ipswitch,MA). Libraries were assessed for concentration and fragment size using the DNA High Sensitivity Assay on the LabChip GX Touch (Perkin Elmer, Waltham, MA). The library concentrations were also assessed by qPCR using the KAPA Library Quantification Kit (Complete, Universal) (Kapa Biosystems, Woburn, MA). The libraries were pooled and sequenced on an  Illumina NovaSeq 6000 using 150bp PE reads (Illumina, San Diego, CA).