A nutritional composition is used to reconstitute an optimal healthy microbiota ecosystem in humans or animals. In particular, an ingestible carrier contains specific amino acids designed to favor the growth of bacteria favorable to individuals health or for reducing the risk of developing deleterious events. In another aspect, specific amino acids are used to reconstitute an optimal healthy microbiota ecosystem in humans or animals, in particular in infants, critically ill patients, in the case of chronic diseases or any stresses impacting the gut and in elderly people.