Comparative immunophenotyping of Saccharomyces cerevisiae and Candida spp. strains from Crohn’s disease patients and their interactions with the gut microbiome

Abstract

Investigation of the fungal communities in animal models of Inflammatory Bowel Diseases (IBD) showed a controversial role of Saccharomyces cerevisiae and Candida spp . In health and disease. These conflicting observations could be ascribed to immunogenic differences among co-specific strains. To assess the relevance of intra-strains differences on yeast immunogenicity and impact on the microbiota, we screened S. cerevisiae and Candida spp. Strains isolated from fecal samples of IBD patients. We compared the cytokine profiles, obtained upon stimulation of Peripheral Blood Mononuclear Cells (PBMCs) and Dendritic Cells with different yeast strains, and evaluated the relationship between strain’s cell wall sugar amount and immune response. Moreover, the gut microbiota composition was explored in relation to fungal isolation from fecal samples by metabarcoding analysis. The comparison of cytokine profiles showed strain dependent rather than species-dependent differences in immune responses. Differences in immunogenicity correlated with the cell wall composition of S. cerevisiae intestinal strains. Stimulation of human healthy PBMCs with different strains showed a pro-inflammatory IL-6 response counterbalanced by IL-10 production. Interestingly, Crohn’s (CD) patients responded differently to “self” and “non-self” strains, eliciting pure Th1 or Th17 cytokine patterns. The differences observed in vitro were recapitulated in vivo , where different strains contributed in dramatically different ways to local epithelial activity and to the inflammation of wild type and Interleukin-deficient mice. Furthermore, we observed that the gut microbiota profiles significantly differentiated according to the presence of Saccharomyces or Candida spp. or the absence of fungal isolates in fecal samples. Our results show the importance to deepen metagenomics and immunophenotyping analyses to the strain level, to elucidate the role of fungal and bacterial communities in health and disease.

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

“…The role of gut mycobiota in IBS was largely ignored so far. There are evidences about its involvement in colitis (Iliev et al 2012), in particular in IBD (Sokol et al 2017;Di Paola et al 2020) and, not last, in stress-induced visceral hypersensitivity (Botschuijver et al 2017). It has also been reported that some metabolic products of yeast metabolism could lead to symptoms related to IBS, and that fungal βglucans of the cell wall that are normally recognized by the host immune system can induce visceral hypersensitivity (Botschuijver et al 2017;Gayathri et al 2020) and differential immune responses (Rizzetto et al 2016;Di Paola et al 2020).…”

“…The gut mycobiota may be involved in IBS and contribute to intestinal hypersensitivity as much as the bacterial counterpart. Future research should be addressed to investigate the potential immunomodulation of IBS fungal isolates, as previously demonstrated in IBD (Di Paola et al 2020), and to evaluate whether bacterial and fungal dysbiosis could act in concert during the gut inflammation in IBS.…”

“…On the other hand, fungi are still under investigation in IBS. Despite being a minor component of the gut microbial community, evidences indicated that fungi can play a role in gut diseases, as demonstrated in inflammatory bowel disease (Iliev et al 2012;Richard et al 2015;Sokol et al 2017;Limon et al 2017;Di Paola et al 2020). Recent evidences, for example, suggested that fungi may partially act in the genesis of visceral hypersensitivity by activating the Dectin-1 receptormediated Syk/CARD9 signaling pathway (Chi et al 2020).…”

The role of mycobiota-genotype association in inflammatory bowel diseases: a narrative review

“…Likewise, Di Paola et al . concluded that the presence of S. cerevisiae was associated with a favorable intestinal environment for beneficial bacterial genera, such as Faecalibacterium ; whereas the absence of normal fungal flora or presence of unusual fungal species were conjugated with the presence of potential pathogenic bacteria that might lead to IBD [ 34 ]. The latest article by Nelson et al reported an increased abundance of Candida sp.…”

“…; n = 5 samples) isolated from 19 CD patients S. cerevisiae is associated with a favorable gut environment for beneficial bacterial genera. Whilst, the absence of yeasts or the presence of other yeast species is connected with potential pathogenic bacteria Di Paola et al [ 34 ] 34 CD patients 47 HS without GI disease PCR primers targeting fecal fungal ITS1 rDNA gene Candida sp. was most associated with CD and Cryptococcus sp.…”