Metagenomic data of Microbial Community from patient stool
Stool was collected in 100% ethanol for nucleic acid extraction as previously described (Lloyd-Price et al., 2019). For DNA extraction, a combination of the QIAamp 96 PowerFecal Qiacube HT Kit (Qiagen Cat No./ID: 51531), the Allprep DNA/RNA 96 Kit (Qiagen Cat No./ID: 80311), and IRS solution (Qiagen Cat No./ID: 26000-50-2) kits were used with a custom protocol as previously described (Kostic, A.D et al. 2015). Briefly, approximately 100 mg of stool was transferred into individual wells of the PowerBead plate, with 0.1 mm glass beads (Cat No./ID: 27500-4-EP-BP) prior to bead beating on a TissueLyzer II at 20 Hz for a total of 10 minutes. Samples were transferred into AllPrep 96-well DNA plates and processed as per manufacturer's instructions. Purified DNA was stored at -20°C. For metagenomic library construction, DNA samples were first quantified by Quant-iT PicoGreen dsDNA Assay (Life Technologies) and normalized to a concentration of 50 pg/L. Illumina sequencing libraries were prepared from 100-250 pg of DNA using the Nextera XT DNA Library Preparation kit (Illumina) according to the manufacturer's recommended protocol, with reaction volumes scaled accordingly. Prior to sequencing, libraries were pooled by collecting equal volumes (200 nL) of each library from batches of 96 samples. Insert sizes and concentrations for each pooled library were determined using an Agilent Bioanalyzer DNA 1000 kit (Agilent Technologies). Libraries were sequenced on HiSeq 2500 2x101 to yield ~10 million paired end reads per sample. De-multiplexing and BAM and FASTQ file generation were performed using the Picard suite (https://broadinstitute.github.io/picard)