Changes in the gut mycobiome in pediatric patients in relation to the clinical activity of Crohn's disease

Table 1 Clinical data from patients with Crohn’s disease and healthy subjects

	Group Ia (n = 50)	Group Ib (n = 16)	Group II (n = 39)	Control (n = 40)
General characteristics
Male:Female (ratio)	29:21 (1.38)	8:8 (1)	22:17 (1.29)	15:25 (0.6)
Age (years), mean ± SD	13 ± 2.9	15 ± 2.8	12.5 ± 4.3	11 ± 4.1
BMI (kg/m2), mean ± SD	17.0 ± 3.1	18.1 ± 2.7	18.1 ± 3.2	18.3 ± 3.8
PCDAI, mean ± SD	34.4 ± 12.7	38.2 ± 18.6	4.1 ± 3.9	N/A
Disease distribution by Paris classification (number of patients)
A1a	4	2	7
A1b	46	14	30
A2	0	2	2
L1	2	1	2
L2	6	2	7
L3	16	4	12
L4aL1	8	2	6
L4aL2	8	3	5
L4aL3	10	4	7
B1	39	11	27
B2	11	5	12

Group Ia: Active/newly diagnosed Crohn's disease (CD); Group Ib: Active/previously diagnosed and treated CD; Group II: Non-active CD; control: Healthy subjects; Paris classification: Age: A1a (0–10 yr), A1b (10–17 yr), A2 (17–40 yr); Location: L1 (distal 1/3 ileum and/or limited cecal disease), L2 (colonic), L3 (ileocolonic), L4a (upper disease proximal to ligament of Treitz), L4b (upper disease distal to ligament of Treitz and proximal to distal 1/3 ileum); Behaviour: B1 (non-structuring non-penetrating), B2 (structuring), B3 (penetrating), B2B3 (both penetrating and structuring disease either at the same or different times); BMI: Body mass index; PCDAI: Pediatric Crohn’s disease activity index; N/A: Not applicable.

Table 2 Alpha diversity metrics P values at the phylum (L2) and species (L7) level, expressed as Shannon, Chao and Fisher indices

Index/group	Shannon		Chao		Fisher
	L2 level	L7 level	L2 level	L7 level	L2 level	L7 level
Ia vs Ib	0.713	0.251	0.836	0.121	0.533	0.312
Ia vs II	0.606	0.584	0.228	0.001a	0.000a	0.011a
Ia vs control	0.000a	0.313	0.006a	0.000a	0.000a	0.000a
Ib vs II	0.492	0.128	0.356	0.185	0.132	0.041a
Ib vs control	0.072	0.053	0.103	0.077	0.072	0.027a
II vs control	0.086	0.710	0.044a	0.631	0.998	0.938

^aP < 0.05, statistically significant value.

Group Ia: Active/newly diagnosed Crohn's disease (CD); Group Ib: Active/previously diagnosed and treated CD; Group II: Non-active CD; control: Healthy subjects.

Table 3 Beta diversity metrics P values at the phylum (L2) and species (L7) level, expressed as Bray-Curtis, Jensen-Shanon and Jaccard indices

Index/group	Bray-Curtis		Jensen-Shannon		Jaccard
	L2 level	L7 level	L2 level	L7 level	L2 level	L7 level
Ia vs Ib	0.753	0.727	0.746	0.92	0.813	0.632
Ia vs II	0.409	0.291	0.404	0.176	0.469	0.389
Ia vs control	0.038a	0.006a	0.009a	0.001a	0.035a	0.008a
Ib vs II	0.532	0.374	0.543	0.468	0.517	0.332
Ib vs control	0.172	0.086	0.125	0.064	0.15	0.094
II vs control	0.313	0.057	0.206	0.026a	0.393	0.087

^aP < 0.05, statistically significant value.

Group Ia: Active/newly diagnosed Crohn's disease (CD); Group Ib: Active/previously diagnosed and treated CD; Group II: Non-active CD; control: Healthy subjects.

Table 4 Correlations of fungal species with patient parameters

Variables/age		Variables/calprotectin		Variables/PCDAI
Debaryomyces hansenii	P < 0.008	Candida dubliniensis	P < 0.003	Candida tropicalis	P < 0.006
	r = -0.08		r = 0.29		r = 0.58
Candida zeylanoides	P < 0.004	Candida sake	P < 0.04
	r = 0.08		r = 0.19

PCDAI: Pediatric Crohn’s disease activity index.