The present invention pertains to a nutritional composition for reconstitutingan optimal healthy microbiota ecosystem in humans or animals. In particular,the present invention relates to an ingestible carrier containing specificamino acids designed to favor the growth of bacteria favorable to individualshealth or for reducing the risk of developing deleterious events. Theinvention also pertains to the use of specific amino acids for reconstitutingan optimal healthy microbiota ecosystem in humans or animals, in particular ininfants, critically ill patients, in the case of chronic diseases or anystresses impacting the gut and in elderly people.