Shotgun metagenomics of human feces: cyclist 005 baseline
Genomic DNA was extracted and purified from 200 mg of fecal matter using the E.Z.N.A. DNA Stool Kit (Ref. D4015-02, VWR, Madrid, Spain). The DNA was quantified using a Qubit fluorometer (Thermo Fisher Scientific, Madrid, Spain). The sequencing libraries used for shotgun metagenomics were generated from 200 ng of purified fecal DNA using Illuminas standard metagenomic library preparation workflow, including DNA fragmentation, end-repair, adaptor ligation, and indexed PCR enrichment. Final libraries were quality-checked and quantified before sequencing. Sequencing was carried out on an Illumina MiSeq platform using the MiSeq Reagent Kit v3 to obtain paired-end 2300 bp reads, yielding high-quality metagenomic data covering the total DNA content of each sample. Raw reads were subjected to standard quality-control procedures, including barcode and adaptor removal, filtering of low-quality bases, and exclusion of chimeric or low-complexity sequences.