This study investigates the relationship between gut microbiota maturity and malnutrition in Bangladeshi children. Using a machine-learning approach, the researchers identified bacterial species that define a healthy gut microbiota during the first two postnatal years. These species were used to develop a model that calculates a 'relative microbiota maturity index' and a 'microbiota-for-age Z-score' to assess the development of a child's fecal microbiota relative to healthy children of similar age. The model was applied to healthy children, children with severe acute malnutrition (SAM), and children with moderate acute malnutrition (MAM). Results show that SAM is associated with significant gut microbiota immaturity, which is only partially improved by two widely used nutritional interventions. The immaturity is also evident in less severe forms of malnutrition and correlates with anthropometric measurements. The study suggests that prolonged interventions with existing or new therapeutic foods and/or gut microbes may be necessary to achieve lasting repair of gut microbiota immaturity in childhood malnutrition and improve clinical outcomes.This study investigates the relationship between gut microbiota maturity and malnutrition in Bangladeshi children. Using a machine-learning approach, the researchers identified bacterial species that define a healthy gut microbiota during the first two postnatal years. These species were used to develop a model that calculates a 'relative microbiota maturity index' and a 'microbiota-for-age Z-score' to assess the development of a child's fecal microbiota relative to healthy children of similar age. The model was applied to healthy children, children with severe acute malnutrition (SAM), and children with moderate acute malnutrition (MAM). Results show that SAM is associated with significant gut microbiota immaturity, which is only partially improved by two widely used nutritional interventions. The immaturity is also evident in less severe forms of malnutrition and correlates with anthropometric measurements. The study suggests that prolonged interventions with existing or new therapeutic foods and/or gut microbes may be necessary to achieve lasting repair of gut microbiota immaturity in childhood malnutrition and improve clinical outcomes.