Gut mycobiome of primary sclerosing cholangitis patients is characterised by an increase of Trichocladium griseum and Candida species

Abstract

We read with interest the recent Gut article by Lemoinne et al describing a dysbiosis of the fungal gut community in faeces of patients suffering from primary sclerosing cholangitis (PSC).1 Though several reports, including our own previous data, support a functional and potentially pathogenic link between the intestinal bacteriota and liver inflammation in PSC,2 3 the aetiology of the disease remains largely unknown.\n\nWe here report on the fungal mycobiome results of our cohort from Northern Germany approved by the local ethics committees (A148/14 and MC-111/15) comprising stool samples of 66 healthy control (HC) subjects, 65 patients with well-characterised PSC (including a subgroup with concomitant colitis (PSC-IBD), n=32) and 38 subjects with UC.3 PCR and sequencing of the fungus-specific internal transcribed spacer 2 genomic region was performed as previously described4 using the primer pair 5.8S-Fun and ITS4-Fun on an Illumina MiSeq machine. Sequencing data were subjected to quality control by using the open source package DADA2 (V.1.10)5 in R (V.3.5.1; https://github.com/mruehlemann/ikmb\\_amplicon\\_processing). Amplicon sequence variants were taxonomically annotated using the UNITE ITS database (V.7.2).6 \n\nIn disagreement with the findings in the French cohort,1 overall fungal alpha diversity in the German cohort was neither altered in PSC nor …