Table 3 Prevalence of bacterial groups in faeces and duodenal biopsies of children

Bacterial group	Prevalence* in faecal samples			p Value χ² test
Bacterial group	Untreated CD (n = 30)	Treated CD (n = 18)	Control (n = 30)	Untreated–treated CD	Untreated CD–control	Treated CD–control
Total count	30/30 (100.0%)	18/18 (100.0%)	30/30 (100.0%)	–	–	–
Bifidobacterium	30/30 (100.0%)	18/18 (100.0%)	30/30 (100.0%)	–	–	–
Bacteroides	30/30 (100.0%)	18/18 (100.0%)	30/30 (100.0%)	–	–	–
Staphylococcus	30/30 (100.0%)	18/18 (100.0%)	25/30 (83.3%)	–	0.026†	0.083
Clostridium coccoides	30/30 (100.0%)	18/18 (100.0%)	30/30 (100.0%)	–	–	–
Clostridium leptum	29/30 (96.6%)	18/18 (100.0%)	30/30 (100.0%)	–	–	–
Lactobacillus	30/30 (100.0%)	18/18 (100.0%)	30/30 (100.0%)	–	–	–
E coli	25/30 (83.3%)	15/18 (83.3%)	15/30 (50.0%)	0.645	0.012†	0.031†
Akkermansia muciniphila	27/30 (90.0%)	15/18 (83.3%)	25/30 (83.3%)	0.658	0.480	0.980

	Prevalence* in biopsy samples			p Value χ² test
	Untreated CD (n = 25)	Treated CD (n = 8)	Control (n = 8)	Untreated–treated CD	Untreated CD–control	Treated CD–control
Total count	25/25 (100.0%)	8/8 (100.0%)	8/8 (100.0%)	–	–	–
Bifidobacterium	25/25 (100.0%)	8/8 (100.0%)	8/8 (100.0%)	–	–	–
Bacteroides	25/25 (100.0%)	8/8 (100.0%)	8/8 (100.0%)	–	–	–
Staphylococcus	13/25 (52.0%)	3/8 (37.5%)	2/8 (25.0%)	0.688	0.241	0.641
Clostridium coccoides	18/25 (72.0%)	4/8 (50.0%)	8/8 (100.0%)	0.391	0.154	0.038†
Clostridium leptum	11/25 (44.0%)	4/8 (50.0%)	4/8 (50.0%)	0.980	0.766	0.980
Lactobacillus	25/25 (100.0%)	4/8 (50.0%)	8/8 (100.0%)	0.002†	–	0.038†
E coli	10/25 (40.0%)	2/8 (25.0%)	2/8 (25.0%)	0.677	0.677	0.715
Akkermansia muciniphila	13/25 (48.0%)	0/8 (0.0%)	2/8 (25.0%)	0.011†	0.241	0.466

*Prevalence (Pr) reflects the number of positive amplifications from total samples analysed by PCR (n = number of samples analysed).
†Statistical differences were calculated by using the χ² test 2×2. Significant difference between groups was established at p<0.050.