Comparative Gut Microbiome Profiles of Stunted and Non-Stunted Children Under Five in Sokoto, Sokoto State: A Metagenomics Approach

Child stunting, a manifestation of chronic undernutrition, is associated with altered gut microbial communities that may perpetuate malnutrition and immune dysfunction. The gut microbiome composition of stunted children in North West Nigeria has not previously been characterized using culture-independent metagenomics. This study compared the gut microbiome profiles of 40 stunted and 40 non-stunted children aged 12 to 59 months attending nutrition clinics in Sokoto, Sokoto State. Stool samples were collected and processed for 16S rRNA gene amplicon sequencing targeting the V3-V4 hypervariable regions using Illumina MiSeq platform. Bioinformatics analysis was performed using QIIME2, with alpha and beta diversity metrics calculated. Linear discriminant analysis effect size (LEfSe) was applied to identify differentially abundant microbial taxa. Results revealed significantly lower alpha diversity in stunted children compared to non-stunted controls. Bacteroidetes-to-Firmicutes ratios were elevated in stunted children, with enrichment of Prevotella copri and depletion of Bifidobacterium longum and Akkermansia muciniphila. Predicted functional metagenomic pathways related to short-chain fatty acid synthesis were significantly reduced in stunted groups. These findings provide the first metagenomics-level description of gut dysbiosis associated with childhood stunting in North West Nigeria and generate candidate microbial biomarkers for nutritional status monitoring and microbiome-targeted intervention development. Keywords: gut microbiome, stunting, metagenomics, 16S rRNA, Sokoto.