Perinatal and Neonatal Manipulation of the Intestinal Microbiome: A Note of Caution


Department of Pediatrics, 1600 SW Archer Road, Human Development Building Room 513, University of Florida, Gainesville, FL 32610; Phone: 352–392–3020; Fax: 352–846–3937; E-mail:


As we learn more about interactions between microbes and the developing gastrointestinal (GI) tract, it is becoming clear that the establishment of the intestinal “microbiome” shortly after birth plays a critical role in the early origins of health and disease. Nutrition, mode of delivery, the use of maternal or postnatal antibiotics, and pre- and probiotics are factors that may alter the microbial ecology and affect lifelong gene expression. Because the neonatal period is a critical period of development when microbes become established in the GI tract, the long-term effects of manipulations of the GI microbial ecology during this time are more amplified than the effects of later manipulations. In this paper, recent research findings are reviewed with the intent of providing information about the benefits of early manipulation of the GI microbiome, but also to give a warning about its indiscriminant manipulation during the perinatal and neonatal time periods.