Small intestinal microbiota in Zambian children with stunting and severe acute malnutrition

Childhood malnutrition is linked to gut microbiome changes; however, most studies focus on faecal samples, while less is known about the small intestinal microbiome. Here, we characterized the duodenal microbiota of children in Zambia with severe acute malnutrition (SAM) and stunting and compared the microbiomes of stunted children living across the globe. To do this, duodenal aspirates from only stunted (i.e. not concurrently wasted) (n = 53) and SAM (n = 24) Zambian children were analysed by 16S rRNA gene amplicon sequencing. Associations between bacterial composition, clinical features and biomarkers of enteropathy were explored. Comparison of duodenal 16S rRNA gene datasets from malnourished children in different countries was also performed using publicly available datasets to assess the impact of age and geography on microbial diversity and composition. The duodenal microbiota in both stunted and SAM children was dominated by Streptococcus, Granulicatella, Gemella and Klebsiella. Children with SAM had lower α-diversity than stunted children. Meta-analysis revealed similarities in the bacterial composition of age-matched children in different countries, but relative abundances and their association with nutritional status differed. This study offers insight into the duodenal microbiota in children with different states of malnutrition, highlighting the potential influence of geography and age in shaping the proximal small intestine. This article is part of the theme issue 'Biological, biomedical and environmental drivers of stunting'.