Gut Microbiota Diversity and Its Association with Malnutrition Severity in East Mediterranean Children Under Five: A Metagenomic Analysis
Nina Weber¹, Clara Hoffmann², Jakob Fischer³, Anna Köhler⁴, Elias Hartmann⁵
Keywords:
malnutrition, gut microbiota, microbiome diversity, child health, metagenomicsAbstract
Childhood malnutrition remains a critical public health concern in the East Mediterranean, affecting 14–21% of children under the age of five. This cross-sectional study evaluated the gut microbiota profiles of 684 malnourished and 312 age-matched well-nourished children across three countries (Sudan, Lebanon, and Egypt) between April 2022 and November 2024. Using 16S rRNA sequencing, we assessed microbial diversity, dominant taxa, and correlations with anthropometric indicators.
Among malnourished children, 61.8% were classified as moderately malnourished (WHZ between -2 and -3), and 38.2% as severely malnourished (WHZ < -3). Shannon diversity indices were significantly lower in severely malnourished children (mean: 1.62 ± 0.21) compared to controls (2.48 ± 0.26, p < 0.001). Bifidobacterium and Faecalibacterium prausnitzii were depleted by 63% and 71%, respectively, in severe cases.
Proteobacteria abundance was markedly higher in severely malnourished children (32.6% vs. 9.4%, p < 0.001), and the Firmicutes-to-Bacteroidetes ratio was inverted (0.68 in malnourished vs. 1.41 in controls). A microbial dysbiosis index (MDI) was calculated and found to correlate inversely with mid-upper arm circumference (r = -0.63, p < 0.001) and serum albumin (r = -0.58, p < 0.001).
Machine learning classification using microbiota profiles yielded an AUC of 0.89 for predicting severe malnutrition, with sensitivity of 84% and specificity of 87%. These findings suggest that gut microbiota analysis could be developed into a diagnostic adjunct for early malnutrition detection and monitoring.
This is the first metagenomic study in the East Mediterranean to link specific microbial patterns with malnutrition severity, providing a foundation for future microbiota-targeted interventions to improve nutritional recovery in vulnerable pediatric populations.
