The co-occurrence of allergic rhinitis (AR) and functional constipation (FC) in pediatric populations presents a considerable clinical burden, with epidemiological studies reporting a comorbidity prevalence of approximately 20% (1, 2). While gut dysbiosis has been extensively characterized in children with either condition alone (3, 4), the specific microbial and metabolic mechanisms underlying their simultaneous presentation remain inadequately elucidated.

Several research gaps persist. First, most FC-related studies have focused on adult populations (2, 5), neglecting pediatric-specific factors such as age-dependent gut microbial maturation and immune plasticity (6, 7). Second, while taxonomic shifts have been described, functional pathway analyses that elucidate microbiota–metabolite–immune crosstalk are limited (3). Third, although probiotics and prebiotics show promise in managing AR or FC individually (4, 8), their synergistic potential in children with AR-FC comorbidity has not been systematically evaluated.

Emerging evidence highlights the microbiota–short-chain fatty acid (SCFA)–immune axis as a key regulator of mucosal and systemic immunity. SCFAs—particularly butyrate, produced by commensals such as Faecalibacterium prausnitzii and Bacteroides stercoris—enhance epithelial barrier function (6), suppress T helper 2 (Th2) responses via histone deacetylase inhibition (9), and promote regulatory T cell(Treg) differentiation (10). In children, SCFA depletion has been linked to barrier disruption, IgE-mediated sensitization, and Th2/Treg imbalance (9). However, the mechanistic connections among gut dysbiosis, metabolic perturbations, and immune alterations in AR-FC comorbidity remain elusive.

To address these gaps, this study integrates taxonomic, functional, and interventional analyses with clinical phenotypes to investigate gut microbiota-driven immune-metabolic disturbances in pediatric AR-FC. We hypothesize that children with AR-FC exhibit a distinct microbial configuration characterized by depletion of SCFA-producing taxa and disruption of metabolic pathways, contributing to epithelial barrier compromise and Th2-skewed immunity. Our findings aim to advance the microbiota–SCFA–immune axis paradigm and support the development of targeted therapies for pediatric AR-FC comorbidity.

Our analysis revealed a distinct gut microbial signature in children with AR-FC comorbidity, characterized by reduced α-diversity (P = 0.003) and significant β-diversity separation (PERMANOVA, P = 0.002).A depletion of key SCFA-producing taxa, including Faecalibacterium prausnitzii and Bacteroides stercoris, was observed alongside an increase in Bifidobacterium abundance. (Figures 2B, 3B). These findings are consistent with previous studies associating Faecalibacterium depletion with impaired mucosal barrier integrity and Th2-driven inflammatory responses in isolated AR or FC (3, 10). Furthermore, the significant separation in β-diversity (PERMANOVA, P = 0.002) between the AR-FC and HC groups underscores that the comorbidity is associated with a distinct overall gut ecosystem structure, extending beyond the depletion of individual taxa.

The observed depletion of SCFA-producing taxa aligns with established mechanisms of immune dysregulation. Smith et al. (14) demonstrated that microbial-derived SCFAs regulate colonic Treg homeostasis via histone deacetylase (HDAC) inhibition, facilitating the expansion of Foxp³⁺ Treg populations. This finding provides mechanistic validation for the inferred immune dysregulation in our cohort, where depletion of SCFA-producing taxa such as Faecalibacterium prausnitzii may be linked to impaired immune tolerance, as supported by established roles of SCFAs in Treg biology (14). Collectively, the observed depletion of SCFA-producing taxa and the associated functional pathway alterations in our cohort are consistent with the proposed microbiota–SCFA–immune axis paradigm (9, 10, 14) in the pathophysiology of AR-FC, though causal relationships require further validation. Additionally, the observed enrichment of Bifidobacterium(Log₂FC = +1.5, P = 0.018) in AR-FC subjects at baseline, despite its conventional association with constipation relief (1), raises critical questions about strain-specific effects. For example, Bifidobacterium longum BB536 has been shown to enhance cell-mediated immunity (15), whereas other Bifidobacterium strains may exert divergent effects under Th2-dominant inflammatory conditions (16). Such heterogeneity highlights the limitation of taxonomic generalization and underscores the need for strain-level resolution when designing probiotic interventions aimed at restoring both gastrointestinal and immune homeostasis.

Functional prediction analysis revealed a distinct metabolic profile in the AR-FC group, characterized by upregulated proteasome activity (P = 0.01) and suppressed LPS biosynthesis (P = 0.02). The increased proteasome activity may enhance luminal antigen processing, potentially promoting IgE sensitization—a hallmark of AR pathophysiology (7). Conversely, suppressed LPS biosynthesis (P = 0.02) may reflect impaired microbial stimulation of innate immunity, potentially reducing TLR4-mediated immune priming and predisposing children to pathogen colonization and chronic inflammation (5, 9). An intriguing finding of our study was the significant upregulation of microbial butanoate and propanoate metabolism pathways in the AR-FC group, as predicted by PICRUSt2, despite a marked depletion of classic SCFA-producing taxa such as Faecalibacterium prausnitzii. This apparent paradox may be explained by several non-mutually exclusive mechanisms. First, microbial community resilience may drive residual taxa to upregulate SCFA-biosynthesis genes in a compensatory manner to maintain metabolic homeostasis—though such efforts may be insufficient to offset the functional loss of high-efficiency SCFA producers. Second, the observed pathway enrichment may not translate into increased SCFA output due to post-transcriptional regulation, limited substrate availability, or disruption of cross-feeding networks essential for efficient SCFA synthesis. Such decoupling between genetic potential and actual metabolic flux has been documented in other dysbiotic conditions. Thus, the functional upregulation may reflect a futile compensatory response or a state of metabolic inefficiency, rather than true SCFA sufficiency. This interpretation, however, requires validation through direct metabolomic quantification of SCFAs in future studies. These findings collectively suggest that the gut microbiota may serve as a potential modulator of the “gut-immune-nose axis,” where dysbiosis is associated with disruptions in both mucosal and systemic immune homeostasis.

The 3-month synbiotic intervention did not induce significant changes in α- or β-diversity. However, several key taxonomic shifts were observed that were in the opposite direction to those seen when comparing HC with AR-FC patients. These included a 54.8% increase in Faecalibacterium abundance (P < 0.05; Figure 5C) and an 85.2% decrease in Bifidobacterium abundance. This finding is consistent with the established role of Faecalibacterium prausnitzii as a primary butyrate producer, which enhances mucosal barrier integrity and promotes intestinal motility through SCFA-mediated mechanisms (14, 17). Although the current study did not directly quantify fecal SCFA levels, the observed Faecalibacterium enrichment, coupled with constipation relief, supports the hypothesis that synbiotic-induced microbial remodeling contributes to functional improvement. In a related study, Erhardt et al. (18) reported that a prebiotic intervention similarly increased fecal SCFA levels and enriched beneficial taxa including Bifidobacterium in subjects with functional constipation, reinforcing the role of fiber-driven microbial modulation in gastrointestinal health. However, the present study extends these observations by demonstrating a direct association between Faecalibacterium expansion and clinical symptom improvement in children with AR-FC comorbidity.

Our investigation identified a pronounced 85.2% reduction in Bifidobacterium abundance following synbiotic intervention. This reproducible pattern across distinct clinical cohorts (19) suggests that diminished Bifidobacterium levels may represent a potential microbial signature of effective constipation relief. The pronounced reduction in Bifidobacterium (−85.2%) may reflect ecological niche competition, as Faecalibacterium and other fiber-fermenting taxa outcompete carbohydrate-preferring Bifidobacteria under high-fiber conditions (20). Although Figure 5D illustrates the post-intervention decline in Bifidobacterium, direct competitive interactions warrant further validation. This trade-off aligns with findings by Scott et al. (20), who demonstrated that Bifidobacterium adolescentis preferentially utilizes fructooligosaccharides over complex fibers. Such strain-specific substrate specialization underscores the importance of developing precision synbiotic formulations that selectively enrich beneficial taxa while preserving microbial ecosystem stability.

Notably, the intervention decreased Escherichia–Shigella—a pathobiont linked to intestinal inflammation—by 12.3%, potentially through competitive exclusion mediated by Lactobacillus strains via bacteriocin production (21). Concomitantly, we observed a functional transition toward enhanced sulfur metabolism (e.g., an 83.2% increase in assimilatory sulfate reduction; Figure 6) and a 35.4% reduction in β-lactam resistance pathways. While these metabolic shifts may reflect microbial adaptation to the synbiotic regime, their direct contribution to clinical symptom improvement remains speculative. Enhanced sulfur assimilation has been previously associated with improved redox homeostasis and mucosal protection (22), whereas the decrease in antibiotic resistance genes may indicate a reduction in potential pathogen load or a shift in microbial community structure under dietary modulation (23). Although prior studies have emphasized butyrate-centered mechanisms in microbiome-targeted therapies for AR (16), our synbiotic intervention appears to have induced a broader spectrum of metabolic changes beyond SCFA production. These functional changes, while mechanistically intriguing, should be interpreted with caution and validated in future studies incorporating metabolomic profiling and larger cohorts.

While the integrated taxonomic, functional, and interventional framework of this study provides valuable mechanistic insights, several limitations should be acknowledged. First, functional prediction analysis were inferred from 16S rRNA gene data using PICRUSt2, an approach that remains inherently predictive and hypothesis-generating rather than confirmatory. The absence of direct SCFA quantification via metabolomic techniques (e.g., LC–MS) represents a key limitation; therefore, future investigations should incorporate targeted metabolomic validation to substantiate the inferred pathway alterations. Second, the cross-sectional study design constrains causal interpretation, underscoring the need for longitudinal analyses to monitor microbiota dynamics throughout AR-FC progression. Third, the relatively small intervention cohort (n = 13) and restricted age range (3–7 years) limit generalizability and reduce statistical power to detect subtle phenotypic effects. Future studies should integrate multi-site cohorts and combine taxonomic, functional, and interventional profiling to comprehensively elucidate the microbiota–SCFA–immune axis in AR-FC comorbidity. Parallel characterization of the nasal (BALT-associated) and intestinal microbiota could delineate site-specific microbial signatures and their roles in disease interplay. Moreover, quantifying mucosal immune mediators—such as secretory IgA (SIgA) and local cytokine networks—in nasal and intestinal secretions would provide essential functional evidence of immune crosstalk (24, 25). Although beyond the current study’s scope, such integrated immuno-metagenomic approaches are crucial to mechanistically link microbial alterations with host immune regulation.

Translational research should prioritize interventions that selectively promote the proliferation and functional activity of Faecalibacterium, potentially through synergistic probiotic formulations (e.g., Lactobacillus rhamnosus GG, known to foster a supportive microbial niche) combined with prebiotic substrates to augment SCFA biosynthesis while mitigating Th2-skewing immune responses. Preclinical validation using germ-free murine models colonized with AR-FC-derived microbiota could delineate causal relationships between Faecalibacterium depletion and nasal hypersensitivity. Future therapeutic strategies could explore optimized SCFAs delivery approaches to enhance local bioavailability in the colon, building upon established roles of butyrate in mucosal immunity (14, 17). However, butyrate may not be the sole mediator of the observed effects; other SCFAs (e.g., propionate, acetate), shifts in sulfur metabolism, or competitive exclusion of pathobionts by probiotic strains may also contribute to the clinical outcomes (20, 21).

This study suggests that gut dysbiosis may represent a potential contributor to pediatric AR-FC comorbidity, marked by the depletion of SCFA-producing taxa (e.g., Faecalibacterium prausnitzii and Bacteroides stercoris) and functional shifts favoring proteasome activity over LPS biosynthesis, a pathway implicated in innate immune regulation. The synbiotic regimen induced taxonomic shifts, including enrichment of Faecalibacterium, which corresponded with constipation alleviation. Conversely, the paradoxical reduction in Bifidobacterium likely reflects competitive substrate utilization, positioning its depletion as a potential biomarker for successful intervention. Functional remodeling post-treatment—including enhanced sulfur metabolism and suppression of antibiotic resistance pathways—demonstrates the adaptive plasticity of gut microbiota under dietary modulation. These alterations implicate disrupted microbial-immune crosstalk along the microbiota–SCFA–immune axis. Translationally, the findings support a dual therapeutic framework: (1) restoration of SCFA-mediated mucosal immunity through targeted synbiotic formulations, and (2) optimization of dietary fiber composition to maintain commensal equilibrium and minimize ecological disruption. Collectively, these findings refine the mechanistic understanding of the microbiota–SCFA–immune axis and provide a foundation for precision microbiome-based therapeutics in pediatric AR-FC provides a well-rounded close linking mechanisms, translational value, and future potential.

Despite these advances, certain limitations, including the small cohort size and reliance on 16S rRNA-based functional inference, necessitate validation through longitudinal, metagenomic, and metabolomic studies. Future interventions should emphasize strain-specific synbiotic formulations designed to promote Faecalibacterium expansion while preserving commensal Bifidobacterium.