1 mm diameter zirconia silica beads

DNA was extracted from stool samples using a mechanical bead-beating approach with the Mini-Beadbeater-16 (BioSpec Products) and 1-mm diameter zirconia/silica beads (BioSpec Products) followed by the QIAamp Fast DNA Stool Mini Kit (Qiagen) according to manufacturer’s instructions. Bead-beating consisted of 7 rounds of alternating 30 s bead-beating bursts followed by 30 s of cooling on ice. For samples subjected to linked-read sequencing, DNA fragments less than ~2 kb were eliminated with a SPRI bead purification approach⁹² using a custom buffer with minor modifications: beads were added at 0.9×, and eluted DNA was resuspended in 50 μl of water. DNA concentration was quantified using a Qubit fluorometer (Thermo Fisher Scientific). DNA fragment length distributions were quantified using a TapeStation 4200 (Agilent Technologies).
Short-read sequencing libraries were prepared with either the Nextera Flex or Nextera XT kit (Illumina) according to manufacturer’s instructions. Linked-read sequencing libraries were prepared on the 10× Genomics Chromium platform (10× Genomics). Linked-read libraries have a single sample index, and were pooled to minimize the possibility of barcode swapping between samples from patients who were roommates (see Supplementary Methods). Libraries were sequenced on an Illumina HiSeq 4000 (Illumina).