Rapid change of infant fecal microbiome

Fifty fecal samples, collected weekly from 5.5 to 17 months of age from an infant who was initially an asymptomatic carrier of C. difficile, were analyzed by 16S rRNA sequencing on a MiSeq. A drastic and permanent change of microbiota composition was observed within 5 days after the transition from human milk to cow milk. A rapid decline and eventual disappearance of C. difficile coincided with weaning at 12.5 months. The bacterial groups that are less abundant in early infancy, and that increase in abundance after weaning, might be responsible for the barrier effect against continued C. difficile colonization.