LAUSR

Significance The intestinal microbiota and environmental enteric dysfunction (EED), an inflammatory syndrome of the small intestine, play a major role in chronic malnutrition. Nevertheless, the microbial changes remain little characterized. Here, we show that increased relative abundance of oral bacteria isolated from the small intestine is associated with reduced abundance of classical small intestinal bacteria. Experimental work further suggests the association of these small intestinal isolates with decreased lipid absorption and increased cell-layer permeability. Further, in the clinical study, we show that EED markers are associated with a decrease in butyrate-producing bacteria and an increase in Fusobacterium and Megasphaera. These findings pave the way for the development of microbiota-targeted interventions and thus, for better treatment of childhood undernutrition in the future.