The gut microbiota of severe acute malnourished and healthy infants in Ghana; a matched case-control study

Background Severe acute malnutrition (SAM) remains a leading cause of child mortality in low-income countries, yet the role of the gut microbiome in its pathogenesis among West African infants remains poorly characterized. This age- and sex-matched case-control study aimed to characterize alterations in the gut microbiota associated with SAM in Ghanaian infants aged 6–23 months. Methods Faecal samples from 19 SAM infants admitted to a Teaching Hospital and 19 healthy controls were analyzed using 16 S rRNA gene sequencing targeting the V3–V4 region. Alpha and beta diversity, taxonomic composition, and microbiota-for-age Z-scores (MAZ) were compared using paired analyses. Results The mean infant age was 15.0 ± 4.33 months (range 8 to 23 months). SAM infants exhibited significantly reduced microbial richness (median OTUs: 33 vs. 75; p = 0.003) and Shannon diversity (2.09 vs. 2.95; p = 0.005). Beta diversity differed markedly between groups (PERMANOVA R² = 0.31, p = 0.0025), with SAM versus healthy status accounting for 4.6% of variation after adjusting for confounders. SAM was characterized by depletion of beneficial genera including Bifidobacterium (18% vs. 30%), Prevotella (11% vs. 20%), and Faecalibacterium (4% vs. 12%), and enrichment of potential pathobionts such as Escherichia-Shigella , Klebsiella and Streptococcus . Microbiota maturity was severely impaired in SAM (median MAZ: −4.72 vs. 0.31 in healthy infants; p = 0.0003). Conclusion SAM is associated with profound gut dysbiosis, characterized by a loss of diversity, expansion of pathobionts, and microbiota immaturity. These findings are hypothesis-generating and suggest that further research is needed to determine whether microbiome-directed interventions could complement nutritional rehabilitation in this population.