Microbiota signatures and genetic risk in pediatric celiac disease

Table 1 Taxonomic changes and functional effects in pediatric celiac disease

Bacterial taxon/group	Reported change	Context/condition	Sample type	Possible functional consequence	Nature of evidence
Bifidobacterium spp.	Decrease	Active CD; may change after GFD	Mostly stool	Decreased SCFA production and interleukin-10-related tolerogenic response; weakened barrier support	Clinical cohort findings + mechanistic support
Lactobacillus spp.	Decrease	Active CD; strain-dependent effect	Stool; in vitro studies	Reduced gluten peptide hydrolysis capacity; increased inflammatory stimulation	Clinical cohort findings + in vitro/functional support
Bacteroides spp.	Increase/variable	Active CD; GFD effect may vary	Stool; duodenal biopsy in some studies	Increased permeability and proinflammatory cytokine responses	Clinical cohort findings + mechanistic interpretation
Proteobacteria	Increase	Active inflammation/dysbiosis	Stool; duodenal biopsy in some studies	Increased oxidative stress, epithelial damage, and inflammation	Clinical cohort findings + mechanistic support
Escherichia coli	Increase	Active CD; strain-dependent	Stool; duodenal biopsy in some studies	Increased virulence-associated epithelial damage and T-cell activation	Clinical cohort findings + strain-dependent support
Staphylococcaceae	Increase	Some pediatric CD cohorts	Mostly stool	Increased dysbiosis, inflammation, and symptom burden	Limited clinical observation
Akkermansia spp.	Decrease/variable	Barrier function; influenced by GFD/age	Mostly stool	Reduced mucus layer and barrier support	Mechanistic support + limited CD-specific findings

CD: Celiac disease; GFD: Gluten-free diet; SCFAs: Short-chain fatty acids.

Table 2 Comparative summary of microbiota studies in pediatric celiac disease

Ref.	Focus area	Key findings	Statistical significance/status
Zafeiropoulou et al[43]	New diagnosis vs GFD	No difference in diversity; GFD effect is dominant	Significant signature in taxon abundance
Olivares et al[54]	Early life and HLA	Impact of HLA-DQ2 on microbial colonization	Significance at the initial stage
Leonard et al[55]	Longitudinal risk monitoring	Microbial shifts occurring 18 months prior to diagnosis	Strong longitudinal significance
El Mouzan et al[56]	Bacteria + virus + fungi	Bacteria and virus combination as a robust diagnostic tool	High AUC value (0.818)
Salamon et al[57]	Bacteria + fungi + HLA	Intermediate microbiota form in siblings; influence of DQ8/DQ2.2	Significant difference in beta diversity

GFD: Gluten-free diet; HLA: Human leukocyte antigen; AUC: Area under the curve.

Table 3 Fungal taxa alterations and their pathophysiological implications in celiac disease

Fungal taxon/group	Reported change	Context/condition	Sample type	Possible functional consequence	Nature of evidence
Candida spp./C. albicans	Increase	Pediatric CD; potential immune cross-reactivity	Stool; duodenal biopsy in some studies	Molecular mimicry via hyphal wall protein 1; possible gliadin cross-reactivity and immune activation	Clinical observation + mechanistic hypothesis
Saccharomyces cerevisiae	Increase/variable	Fungal dysbiosis; inflammation-associated context	Mostly stool	ASCA-related immune response; marker of intestinal fungal dysbiosis	Clinical observation + immunological association
Tricholomataceae	Increase	Pediatric CD-associated fungal signature	Fecal samples	Possible marker of altered fungal community structure	Study-dependent clinical observation
Saccharomycetaceae	Increase	Family-level fungal shift in CD	Mostly stool	Fungal ecosystem imbalance; possible dysbiosis marker	Clinical observation + ecological interpretation
Pichia kudriavzevii	Decrease	Loss of commensal fungal diversity	Mostly stool	Reduced protective microbial competition; weakened fungal ecosystem balance	Limited clinical observation + ecological interpretation
Pneumocystis jirovecii	Decrease	Duodenal mucosal fungal profile	Duodenal biopsy	Possible altered mucosal fungal niche; unclear functional relevance	Study-dependent mucosal finding
Fungal community overall	Altered/variable	Active CD, at-risk siblings, and preclinical context	Stool; duodenal biopsy in some studies	Barrier regulation, antigenic environment, T-cell polarization, and immune tolerance	Clinical cohort findings + mechanistic support

CD: Celiac disease; ASCA: Anti-Saccharomyces cerevisiae antibodies.