Whole shotgun metagenomic sequencing for 1,679 individuals (2,075 samples) from the TwinsUK cohort. Supporting data for: Pope et al, Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.
Library preparation was performed manually using the Nextera XT protocol (Illumina, PN. 15031942). DNA concentrations were measured with the Quant-iT Picogreen assay (Life Technologies, PN. Q33120) on an AF2200 plate reader (Eppendorf) and adjusted to 0.2 ng/µL for each library. DNA was then fragmented and tagged through tagmentation, followed by PCR amplification on a Veriti 96-well thermocycler (Applied Biosystems). Libraries were purified using AMPure XP beads (Beckman Coulter, PN. A63880), and the size distribution of fragments was checked using a Labchip GX Touch HiSens. Sequencing was carried out by GenomeScan (https://genomescan.nl/) using an Illumina HiSeq 2500 with a read length of 2 × 125 bp.  Prior to uploading, and due to privacy concerns, human reads were removed using a human reference. Low-complexity sequences and highly conserved features (e.g., ribosomal sequences), which are shared across species, were also removed to avoid false-positive matches. This file is available within our processing pipeline (https://github.com/alesssia/YAMP) and can be downloaded from Zenodo (https://zenodo.org/records/4629921#.YFnf50j7SL4).  Meta data are available by application to the Twin Research Executive Access committee (TREC) at King's College London. The TwinsUK BioResource is managed by TREC, which provides governance of access to TwinsUK data and samples. TwinsUK data users are bound by data sharing agreement set out in the data access application form, which includes responsibilities with respect to third party data sharing and maintaining participant privacy. Further responsibilities include a responsibility to acknowledge data sharing.