The human microbiota, a collection of microorganisms mostly settled in the gastrointestinal tract, plays a major role in the maintenance of the hosts' health and in development of disease as well. Exposure to different conditions early in life contributes to distinct "pioneer" bacterial communities, which shape the newborn infants' development and influence their later physiological, immunological and neurological homeostasis. Newborn infants with congenital malformations of the gastrointestinal tract (CMGIT), necrotizing enterocolitis (NEC), and spontaneous intestinal perforation (SIP) commonly require abdominal surgery and enterostomy. While intestinal microbiota has been extensively studied in infants with anatomically uninterrupted intestine, the knowledge of longitudinal intestinal colonization in this population is scarce.

This is an exploratory, observational, and longitudinal prospective study, primarily aimed to determine longitudinally the colonization of the proximal remnant intestine, in newborn infants with enterostomy after surgery (three weeks) for CMGIT, NEC and SIP. The secondary aim is to explore the associations of the colonization with the mode of delivery, gestational age, postnatal age, duration of fasting, type of enteric feeding, antimicrobial therapy, H2-receptor antagonist therapy, and length of proximal remnant intestine.

Inclusion criteria: newborn infants with enterostomy after surgery for CMGIT, NEC or SIP, consecutively admitted

Exclusion criteria: newborn infants with diagnosed inborn errors of metabolism, those whose parents or legal guardians will not consent to participate or withdrawn the consent, and those who had not complete 21 days of follow-up.

Newborn infants with enterostomy after surgery for CMGIT, NEC or SIP recruited at the NICU of Hospital Dona Estefânia, Centro Hospitalar de Lisboa Central, Lisbon, Portugal.