Chronic malnutrition, manifesting in stunted growth, affects one out of four children worldwide and has severe long-term sequelae including diminished corporal and cognitive development. Nevertheless, little research has been performed on its etiology and current treatment interventions only partially correct the encountered pathophysiological disturbances. Recent work suggests that the microbiota and an inflammatory syndrome of the small intestine, called environmental enteric disease (EED) play an important major role in the syndrome. In order to elucidate the (small) intestinal dysbiosis and its role in the pathophysiological mechanisms, we performed a cross-sectional study in Antananarivo (Madagascar) and Bangui (Central African Republic) recruiting 1’000 children aged 2-5 years (Afribiota project) and modeled the pathophysiological changes subsequently in cell culture and animal models to shed light on the underlying pathophysiological mechanisms. This allowed us to unravel a new microbial signature associated with stunted child growth and to show its implication in both, inflammation as well as malabsorption.