The fecal mycobiome in patients with Irritable Bowel Syndrome

Abstract

Alterations of the gut microbiota have been reported in various gastrointestinal disorders, but knowledge of the mycobiome is limited. We investigated the gut mycobiome of 80 patients with Irritable Bowel Syndrome (IBS) in comparison with 64 control subjects. The fungal-specific internal transcribed spacer 1 (ITS-1) amplicon was sequenced, and mycobiome zero-radius operational taxonomic units (zOTUs) were defined representing known and unknown species and strains. The fungal community was sparse and individual-specific in all (both IBS and control) subjects. Although beta-diversity differed significantly between IBS and controls, no difference was found among clinical subtypes of IBS or in comparison with the mycobiome of subjects with bile acid malabsorption (BAM), a condition which may overlap with IBS with diarrhoea. The mycobiome alterations co-varied significantly with the bacteriome and metabolome but were not linked with dietary habits. As a putative biomarker of IBS, the predictive power of the fecal mycobiome in machine learning models was significantly better than random but insufficient for clinical diagnosis. The mycobiome presents limited therapeutic and diagnostic potential for IBS, despite co-variation with bacterial components which do offer such potential.

Gut microbiota profiles and characterization of cultivable fungal isolates in IBS patients

“…By using the culturomics approach, we confirmed an imbalanced fungal community in accordance with results from Gu et al (2019) and Das et al (2021). In both our cohorts, the most abundant fungal species was C. albicans, isolated at higher frequency in IBS patients than HS.…”

“…In humans, Das et al (2021) showed that the mycobiome composition differentiates patients with IBS from controls, with a significant co-variation between mycobiota and bacteriome. Sokol et al (2017) showed increased intermicrobial kingdom relationship in ulcerative colitis, and reduced interactions between gut bacteria and fungi in Crohn's disease, while results from Imai et al (2019) showed the contrary.…”

“…We identified enrichment of Saccharomycetes in IBS compared HS. In general, fungal metagenomics procedure suffers from some limitation, especially due to the wide variance in the mycobiome taxonomic composition, as highlighted by Das et al (2021), which suggest to consider sequencing both the ITS1 and ITS2 regions.…”

“…In general, the specific mechanisms of the mycobiome involved in IBS yet remain to be clarified. Critical issue has been raised about the potential contribution of gut mycobiota analysis for diagnostic usefulness, although a pathogenetic importance of the mycobiota in IBS was recognized (Das et al 2021).…”

The Gut-Liver Axis in Cholestatic Liver Diseases

“…Dysbiosis of the fungal microbiome and involvement of fungi in the pathogenesis of disease has been demonstrated for IBD, colorectal cancer, obesity, and atherosclerosis [236,[244][245][246][247][248][249][250][251], while patients with diabetes mellitus type 1 demonstrated increased fungal diversity [252]. For IBS, fungal dysbiosis was linked to increased intestinal hypersensitivity while the added value of the investigation of the mycobiome for diagnostic or therapeutic aims was doubted in one study [253,254]. Concerning liver diseases, changes of the mycobiome characterized by lower diversity and Candida overgrowth for ALD and by lower diversity and distinct fungal composition in NAFLD were demonstrated [235].…”