Table 1 IBD affecting intestinal mycobiota in IBD patients

57 IBD patients

47 HS

Intestinal mucosa

18S rDNA-based sequencing

Significant higher fungal diversity in patients with CD in comparison with HS. No disease-specific fungal species were found in the CD and UC group

Ott et al. [28]

41 CD families composed of: 129 patients and 113 healthy relatives

14 healthy controls families composed of 76 individuals

Mouth swabs and Stool samples were processed using chromogenic medium. Mouth swabs were rubbed directly onto the medium. Stool samples were taken with an inoculation loop. Plates were incubated for 48 h at 37°℃C. The yeast species were differentiated using the specific color of the colonies. Presumptive identification of yeast species was confirmed by either Bichro-Latex-albicans for C. albicans, or the API 32C system for other species

Top most prevalent mycobiome in CD patients: C. albicans mouth [26 (34.7%)] stool [13( 22%)]

C. glabrate mouth [3 (4%)], stool [1 (1.7%)]

C. tropicalis mouth [1 (1.3%)], stool 0

Standaert-Vitse et al. [22]

19 patients with active CD

7 HS

PCR targeting fecal fungal 18S rDNA gene

Decreased S. cerevisiae and overrepresented Aspergillus clavatus, C. albicans, and Cryptococcus neoformans proportions were present in CD patients

Li et al. [13]

90 children with CD

26 HS children

Sequence was acquired using the Illumina HiSeq method (Illumina)

Five yeasts including, S. cerevisiae, C. lusitaniae, Pichia jadinii (also known as and C. utiliz), C. albicans, and Kluyveromyces marxianus were positively associated with CD, particularly in the setting of greater bacterial dysbiosis

Lewis et al. [29]

32 patients with IBD

90 HS

PCR primers targeting fecal fungal the ITS rDNA gene

IBD samples had significantly lower fungal diversity The most commonly observed fungi were C. Pichia jadinii. C. parapsilosis, was also more common in the pediatric IBD samples. Cladosporium cladosporioides, was more common in HS

Chehoud et al. [30]

9 multiplex families comprising 20 CD patients and their 28 cohabiting NCDR

4 unrelated healthy families 21 individuals with no history of CD (NCDU) living in the same geographic area

PCR primers targeting fecal fungal ITS1 rDNA gene

Increased richness in the NCDU group compared to the CD or NCDR group but no difference in the mycobiome richness of CD patients and their healthy relatives. S. cerevisiae tended to increase in healthy (NCDR) individuals. C. tropicalis was significantly abundant in CD compared to NCDR group

Hoarau et al. [31]

23 CD patients (16 in flare, 7 in remission)

10 HS

Colonic mucosa ITS2, 16S, and 18S rDNA sequencing

Global fungi load was significantly increased in both inflamed and non-inflamed mucosa compared to HS. However, no significant differences in fungal diversity between the studied groups were observed

Liguori et al. [12]

25 children with IBD

12 HS

Colonic mucosa

18S rDNA sequencing

A shift from the Ascomycota-predominant microbiota in HS to a different fungal spectrum with Basidomycetes predominance in patients with de-novo IBD

Mukhopadhya et al. [32]

235 IBD patients

38 HS

PCR primers targeting fecal fungal ITS2 rDNA gene

S. cerevisiae reduction in patients with IBD (vs. healthy controls) and with flare (vs. remission). Higher Basidiomycota-to-Ascomycota abundance ratio in patients with IBD in flare (either UC or CD) but normal ratio in remission

Sokol et al. [8]

14 UC patients15 HS

PCR primers targeting fecal fungal ITS1 and ITS2 rDNA gene

Wickerhamomyces, an unidentified genus of Saccharomycetales, Aspergillus, Sterigmatomyces, and Candida sp. showed an increasing trend in UC patients compared with HS. There was a marked difference in Aspergillus abundance between the groups. The proportions of Ascomycota and Basidiomycota were not significantly different between the groups

Qiu et al. [11]

93 pediatric; 34 CD, 27 UC patients, 32 HS

PCR primers targeting fecal fungal ITS1-5.8-S-ITS2 regions of rDNA gene

S. cerevisiae (n = 7 fecal samples) and other yeasts (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. with non-CD. The Basidiomycota/Ascomycota abundance ratio was found to be significantly lower in CD patients

Nelson et al. [35]