Integrated multi-omics analysis reveals distinct metabolic signatures and gut microbiome alterations across the pediatric obesity spectrum

Pediatric obesity drives extensive metabolic remodeling across gut and systemic compartments, yet integrated multi-omics characterization across the full obesity spectrum remains incomplete. We studied 57 Mexican children stratified by BMI into normal weight (NW, n = 15), overweight (Ow, n = 8), and obese (Ob, n = 34) groups using liver enzyme profiling, untargeted fecal and serum metabolomics, 16S rRNA gut microbiome sequencing, and antimicrobial resistance assessment. Demographic parameters were comparable across groups (p = 0.632), minimizing confounding. Gamma-glutamyl transferase (GGT) showed the strongest obesity association (25.5 ± 6.0 vs. 15.0 ± 3.0 U/L in NW; p < 0.001), outperforming ALT and AST as an early hepatic stress biomarker. Metabolomic profiling identified 1088 altered fecal and 1041 altered serum metabolites (Ob vs. NW), with enriched pathways spanning aromatic amino acid metabolism, one-carbon metabolism, glycolysis/TCA cycle, and nucleotide biosynthesis. Key perturbations included upregulation of kynurenine and 3-nitrotyrosine alongside downregulation of bile acids and purine metabolites. 16S rRNA sequencing revealed 78, 95, and 28 differentially abundant taxa in Ow vs. NW, Ob vs. Ow, and Ob vs. NW comparisons, with elevated beta-diversity dispersion in obesity. Co-abundance network analysis uncovered disrupted metabolite–metabolite and taxon‒taxon interactions, including loss of beneficial SCFA-producing consortia, bile acid dysregulation, and altered amino acid-microbiome coupling. Integration of microbiome and metabolome data revealed high-magnitude genus-metabolite correlations—including Lachnospiraceae with acetate (ρ = 0.92) and Tyzzerella with vulpecholate (ρ = 0.94)—mapping to mechanistic pathways linking SCFAs, bile acids, tryptophan-indole derivatives, and aromatic amino acids to obesity pathogenesis. These findings identify GGT as a sensitive pediatric metabolic biomarker and provide mechanistic insights and therapeutic targets for early intervention.