Gut microbial diversity impacts carbohydrate fermentation by children with severe acute malnutrition

African children suffering from severe acute malnutrition (SAM) have a disrupted gut microbiome and low short-chain fatty acids (SCFAs). These are linked to persistently high mortality and morbidity rates. Supplementing recovery feeding regimes with suitable fermentable carbohydrate may improve outcomes in SAM. We adapted in vitro colon models to investigate the ability of children with SAM to utilize four carbohydrate substrates: milk powders (with and without human milk-like oligosaccharides), chickpea-enriched feed, and inulin. All substrates, except inulin, were fermented to produce SCFAs. The inability to utilize inulin ex vivo, a widely used prebiotic, is attributed to low microbial diversity, enriched with Proteobacteria. Stool samples obtained after partial anthropometric recovery showed increased microbial diversity and higher levels of GH32 enzyme family, responsible for inulin metabolism. These findings can inform the design of future therapeutic feeds for the treatment of SAM, where inulin has been found ineffective during initial hospitalization. Alternative carbohydrates appear to be more effective in supporting gut recovery during both the initial and later treatment phases.