Fecal samples from individuals were centrifuged at 400g. Pellets were collected for fungal DNA isolation. Pellets were treated with 200 U per ml lyticase (Sigma-Aldrich) followed by bead beating, and processing using the Quick-DNA Fungal/Bacterial Kit (Zymo Research). Fungal DNA presence was validated by RTPCR for fungal 18S. Fungal ITS1-2 regions were amplified by PCR using the following primers with sample barcodes and sequencing adaptors. Fungal primers: ITS1F, CTTGGTCATTTAGAGGAAGTAA; ITS2R, GCTGCGTTCTTCATCGATGC; forward overhang, 5' TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-[locus-specific sequence]; reverse overhang, 5' GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-[locus-specific sequence].  ITS amplicons were generated with 35 cycles using Invitrogen AccuPrime PCR reagents (Carlsbad). The amplicons were then used in the second PCR reaction, using Illumina Nextera XT v2 (Illumina) barcoded primers to uniquely index each sample. DNA was amplified using the following PCR protocol: initial denaturation at 94C for 10 min; followed by 40 cycles of denaturation at 94C for 30 s, annealing at 55C for 30 s and elongation at 72C for 2 min; followed by an elongation step at 72C for 30 min. All libraries were processed for quality control using the DNA 1000 Bioanalyzer (Agilent), and Qubit (Life Technologies) to validate and quantify library construction before preparing a paired-end flow cell. Clonal bridge amplification (Illumina) was performed using a cBot (Illumina). Finally, sequencing-by-synthesis was performed using the Illumina MiSeq platform (Illumina).