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Introduction: This study evaluated nutrient deficiencies in infants and toddlers with inflammatory bowel disease (IBD) and eosinophilic gastrointestinal disorders (EGID), whose primary nutritional source is elemental formulas (EFs). Methods: The nutrient status of children with IBD and EGID aged 6 months to 6 years was evaluated. Results: Twenty-one children fed with EFs (EF group) and 25 controls (CL group) were enrolled. The selenium level in the EF group was lower than that in the CL group (2.2 µg/dL vs. 9.3 µg/dL; p<0.01). Although fat-soluble vitamins were deficient in some EF group participants, no significant differences were observed in their concentration and insufficiency proportion. However, ascorbic acid deficiency was more frequent in the EF group, with significantly lower levels (8.6 µg/mL vs. 12.0 µg/mL; p<0.01). The triene:tetraene ratio was significantly higher in the EF group (0.046 vs. 0.010; p<0.01). Asparagine and taurine levels were significantly lower in the EF group (asparagine: p<0.01; taurine: p<0.01) and tyrosine and phenylalanine levels were higher in the EF group, resulting in a lower Fisher’s ratio (p<0.01). Conclusion: Long-term feeding with EFs can cause deficiencies in essential fatty acids, selenium, and ascorbic acid and also carries a risk of amino acid imbalance in infants and toddlers.

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