Inflammatory bowel diseases (IBD), particularly Crohn’s disease and ulcerative colitis, are increasingly recognized among children and adolescents, with rising incidence reported globally. Pediatric IBD presents distinct challenges due to its impact on growth, development, and quality of life. Nutritional therapies, especially exclusive enteral nutrition (EEN), have emerged not only as supportive care but as front-line therapeutic strategies for inducing remission, reducing inflammation, and modulating the gut microbiota¹˒².

The concept of precision nutrition—tailoring dietary interventions based on individual genetic, microbiome, and metabolic profiles—has gained considerable momentum in pediatric IBD research. Emerging studies suggest that specific dietary components can directly influence mucosal healing, microbial composition, and immune regulation³˒⁴. Personalized dietary protocols, such as the Crohn's Disease Exclusion Diet (CDED), partial enteral nutrition (PEN), and microbiota-directed diets, are increasingly being integrated into clinical care⁵˒⁶.

While exclusive enteral nutrition remains the gold standard for inducing remission in pediatric Crohn’s disease, there is growing evidence that its mechanisms of action extend beyond bowel rest, involving shifts in microbial taxa and metabolite signatures⁷˒⁸. Newer approaches are investigating combinations of biologics with precision-formulated enteral regimens to enhance efficacy and minimize side effects⁹.

This study aims to evaluate the effectiveness of a structured, microbiota-targeted nutritional protocol in pediatric IBD patients and to identify predictors of clinical response. The findings aim to contribute to the evolving framework of personalized nutrition in pediatric inflammatory conditions.

Study Design and Setting

This was a prospective observational study conducted at a tertiary pediatric gastroenterology center in India. Ethical clearance was obtained from the institutional ethics committee, and written informed consent was obtained from all parents/guardians.

Participants

Children aged 6–17 years with a confirmed diagnosis of Crohn’s disease or ulcerative colitis (per revised Porto criteria) were recruited. Inclusion criteria included mild-to-moderate disease activity (PCDAI or PUCAI scores between 10–40), stable medical therapy for the past 4 weeks, and no prior enteral nutrition within the last 3 months. Exclusion criteria included severe disease requiring hospitalization, corticosteroid use within 4 weeks, and known food allergies.

Nutritional Intervention

All participants received a personalized precision nutrition plan developed using clinical history, dietary recall, and baseline microbiota profiling. The intervention comprised:

• Phase 1: 6 weeks of microbiota-directed exclusive enteral nutrition (polymeric formula)
• Phase 2: 6 weeks of a maintenance diet (CDED-style with tailored macronutrient ratios)

Nutritional formulas were supplied under supervision, and dietary adherence was reinforced via teleconsultation and weekly dietitian monitoring.

Outcome Measures

The primary outcome was clinical remission, defined as PCDAI <10 or PUCAI <10 at week 6 and sustained through week 12.

Secondary outcomes included:

• Change in inflammatory markers (CRP, ESR, fecal calprotectin)
• Change in BMI z-score
• Microbiota shifts (via 16S rRNA sequencing at baseline and week 12)
• Adherence score and tolerance (parent-reported)

Statistical Analysis

Descriptive statistics were calculated for demographic and clinical variables. Paired t-tests and ANOVA were used to assess within-group and between-group changes. Microbial diversity was analyzed using QIIME2 software, and associations were evaluated using PERMANOVA. A p-value of <0.05 was considered statistically significant.

Table 1: Baseline Characteristics of Pediatric IBD Patients (n = 50)

Table 2: Clinical Outcomes at Week 6 and Week 12

Table 3: Adherence and Tolerance Outcomes

This study provides evidence supporting the feasibility and effectiveness of precision nutrition in the management of pediatric inflammatory bowel disease (IBD). Our findings align with the evolving paradigm that diet is not just supportive but therapeutic, particularly when interventions are personalized based on microbiota profiles, disease phenotype, and inflammatory status¹˒².

The observed remission rates at weeks 6 (68%) and 12 (62%) are consistent with previous reports on exclusive enteral nutrition (EEN) as a first-line induction therapy³. Importantly, our study integrated microbiota-targeted strategies, echoing recent ESPGHAN recommendations that advocate for dietary personalization in pediatric IBD to improve both efficacy and tolerability⁴. While EEN alone has been known to modify gut microbial composition favorably⁵˒⁶, its combination with exclusion diets or tailored macronutrient modulation—as applied here—enhances clinical sustainability and adherence⁷˒⁸.

Reductions in fecal calprotectin and CRP levels further support the anti-inflammatory effect of dietary modulation. These markers correlate well with mucosal healing, the gold standard for long-term remission in IBD management⁹˒¹⁰. The increase in BMI z-scores over the 12-week period also suggests that nutritional repletion can be achieved without compromising disease control¹¹.

Our study reinforces that adherence plays a pivotal role in success. With over 80% of participants completing the intervention, the personalized approach likely contributed to better tolerance and engagement. This aligns with multicenter observations that tailoring interventions to patient lifestyle and preferences improves long-term outcomes¹²˒¹³.

Moreover, microbiota-based stratification—though still exploratory—has shown potential to predict responsiveness to dietary therapy¹⁴. Previous research has demonstrated distinct enterotype shifts following dietary interventions, with increases in short-chain fatty acid-producing bacteria linked to clinical remission¹⁵˒¹⁶. Our future analysis will focus on the microbiome samples collected to investigate these patterns further.

The implications of our findings are twofold. First, integrating dietitians and microbiome profiling into routine pediatric IBD care is essential. Second, greater effort is needed to define standardized, evidence-based precision protocols for different IBD subtypes and severities¹⁷˒¹⁸. Although biologics remain indispensable in moderate-to-severe disease, diet-first strategies may reduce drug burden and costs when applied early and appropriately¹⁹.

Limitations of this study include its single-center design and short-term follow-up. While biochemical and clinical markers improved, endoscopic confirmation of mucosal healing was not available. Additionally, adherence self-reporting and parental recall introduce bias. However, the strengths of the study lie in its prospective design, stratified dietary approach, and comprehensive assessment framework.

Our results, supported by prior evidence, confirm that precision nutrition represents a transformative approach in pediatric IBD care, not just as adjunctive but as front-line therapy²⁰-25.

Precision nutrition, tailored to individual microbiota and disease profiles, offers a promising and practical strategy for managing pediatric inflammatory bowel disease. This study demonstrates that a personalized, microbiota-targeted dietary approach can achieve high remission rates, improve nutritional status, and reduce inflammatory markers. Importantly, it also shows that such interventions are well-tolerated and feasible in real-world settings.

Future research should focus on refining stratification tools, integrating omics-based dietary algorithms, and conducting multicenter trials to validate the long-term outcomes. Meanwhile, clinicians should be encouraged to incorporate precision nutrition early in the therapeutic cascade for pediatric IBD.

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