Gut mucosal mycobiome profiling in Crohn's disease uncovers an AMP-mediated anti-inflammatory effect of Cladosporium sphaerospermum.

C. sphaerospermum is significantly depleted in the ileal mucosa of CD patients compared to healthy individuals, but remains unchanged in faeces.

• Patients with CD and healthy individuals were enrolled from three independent cohorts
• Multi-omics profiling was conducted on ileal mucosal mycobiome and bacteriome, along with faecal mycobiome, bacteriome and metabolome
• The depletion was specific to the mucosal compartment, with faecal levels showing no significant difference between CD patients and healthy controls
• This finding highlights the importance of compartment-specific sampling when studying gut mycobiome alterations in disease

C. sphaerospermum occupies the intestinal crypt niche in the gut mucosa.

• Causality studies were conducted to determine the physical localization of C. sphaerospermum
• The fungus was found to occupy the intestinal crypt niche specifically
• This localization was demonstrated as part of characterizing the functional role of this mucosa-associated fungus

C. sphaerospermum counteracts intestinal inflammation partly through adenosine 5'-monophosphate (AMP) production.

• The anti-inflammatory effect of AMP production by C. sphaerospermum was demonstrated in mouse models, in vitro experiments, and fungal cultures
• AMP was identified as a key metabolite mediating the anti-inflammatory properties of C. sphaerospermum
• The anti-inflammatory effect was described as 'partly' mediated by AMP, suggesting additional mechanisms may also be involved

C. sphaerospermum upregulates epithelial cell junctions and the Wnt signalling pathway as part of its anti-inflammatory mechanism.

• Mechanistic studies revealed upregulation of epithelial cell junctions following C. sphaerospermum exposure
• The Wnt signalling pathway was also upregulated, providing a mechanistic basis for the observed anti-inflammatory and mucosal protective effects
• These findings suggest C. sphaerospermum promotes intestinal barrier integrity in addition to reducing inflammation

The gut mucosal mycobiome of the small bowel, including the ileal mucosa, had not been well characterized in CD prior to this study.

• The fungi of the small bowel mucosa and their metabolic functions, 'particularly protective ones, remain largely unexplored'
• CD most commonly affects the terminal ileum, making this an important but understudied compartment
• The study addresses a gap by profiling both ileal mucosal mycobiome and bacteriome alongside faecal counterparts

C. sphaerospermum is identified as a mucosa-associated beneficial fungus with potential as a novel microbial intervention strategy for CD.

• The study suggests C. sphaerospermum represents a 'mucosa-associated beneficial fungus'
• The authors propose this finding suggests 'potential novel microbial intervention strategies for CD'
• The combination of depletion in disease and demonstrated anti-inflammatory function in experimental models supports a protective role