Characterising the Gut Microbiome in Nigerian Children with Severe Acute Malnutrition: Implications for Recovery Trajectories and Therapeutic Food Response

Severe acute malnutrition in Nigerian children is associated with profound gut microbiome disruption, yet the specific microbial compositional and functional signatures in the Nigerian context, their relationship to recovery trajectories, and their modulation by ready-to-use therapeutic foods have not been characterised at metagenomic resolution. This study characterises the gut microbiome of Nigerian children with severe acute malnutrition and examines its association with recovery trajectory and therapeutic food response. A prospective longitudinal design recruits 400 children aged 6 to 59 months with confirmed SAM across four outpatient therapeutic programme sites in Kano, Sokoto, Yobe, and Zamfara States. Stool samples are collected at enrolment, week 4, and discharge, with shotgun metagenomic sequencing performed using Illumina NovaSeq. Microbial community composition is analysed using QIIME2, and functional pathway reconstruction is performed using HUMAnN3. Host intestinal inflammation is assessed by faecal calprotectin and neopterin. Recovery trajectory is defined by MUAC increment per week and weight-for-height Z-score recovery. Mixed-effects regression models in R examine microbial predictors of recovery speed and non-response to RUTF. Dietary diversity before admission is examined as an effect modifier. The Gut Microbiome-Nutrient Sensing Theory and the Ecological Succession Model of microbiome recovery provide the theoretical framework. Original contributions include the first metagenomic characterisation of SAM gut microbiome in Nigerian children and a validated microbial signature predicting RUTF non-response. Findings will inform next-generation SAM therapeutic food development. Keywords: severe acute malnutrition, gut microbiome, metagenomics, therapeutic food, North West Nigeria.