The duodenal microbiota of Zambian children with severe acute malnutrition and stunting was dominated by Streptococcus, Granulicatella, Gemella and Klebsiella, with SAM children showing lower α-diversity than stunted children, and meta-analysis revealing similarities in bacterial composition across countries but differing relative abundances associated with nutritional status.
The duodenal microbiota of both stunted and SAM Zambian children was dominated by Streptococcus, Granulicatella, Gemella, and Klebsiella.
Children with severe acute malnutrition had lower α-diversity in duodenal microbiota compared to stunted children.
Associations were found between bacterial composition and clinical features and biomarkers of enteropathy in malnourished children.
Meta-analysis of duodenal 16S rRNA gene datasets revealed similarities in bacterial composition of age-matched malnourished children across different countries, but relative abundances and their association with nutritional status differed.
Most existing studies on gut microbiome in childhood malnutrition focus on fecal samples, and this study addresses a gap by characterizing the small intestinal (duodenal) microbiome.
This research suggests that in Zambian children suffering from malnutrition — whether stunting (being too short for their age) or severe acute malnutrition (SAM, which involves both stunting and wasting) — the upper part of the small intestine harbors a distinctive mix of bacteria, predominantly Streptococcus, Granulicatella, Gemella, and Klebsiella. Importantly, children with the more severe form of malnutrition (SAM) had less variety in their gut bacteria compared to children who were only stunted. The researchers obtained this information by directly sampling fluid from the duodenum (the first part of the small intestine), which provides a more direct picture of small intestinal bacteria than the stool samples used in most previous studies. When the researchers compared their Zambian data with publicly available data from malnourished children in other countries, they found that while the types of bacteria present were broadly similar in age-matched children regardless of geography, the exact proportions of those bacteria and how they related to nutritional status differed by country. This suggests that both a child's age and where they live play a role in shaping their small intestinal microbiome. This research matters because it deepens our understanding of how gut bacteria differ in children with varying degrees of malnutrition and highlights the small intestine — not just the large intestine — as an important site of microbial changes. Understanding these differences could eventually help researchers develop targeted nutritional or microbiome-based interventions for malnourished children, while also underscoring that such interventions may need to be tailored to local contexts given the geographic differences observed.
Mweetwa M, Ashan K, Kung V, McNulty N, Besa E, Barratt M, et al.. (2026). Small intestinal microbiota in Zambian children with stunting and severe acute malnutrition.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. https://doi.org/10.1098/rstb.20250088