Neonatal gut microbiota establishment. human gut metagenome

The establishment of a pioneer gut microbiota is increasingly recognized as a crucial stage in neonatal development influencing health throughout life. While current knowledge is mainly based on either culture or molecular analysis of feces, we opted for a comprehensive approach complementing culture with state-of-the-art molecular methods. The bacterial composition in feces from seven healthy vaginally-delivered, breast-fed neonates was analyzed at days 4-6, 9-14 and 25-30 postnatal, using culture, 16S rRNA gene sequencing of isolates, qPCR and 454-pyrosequencing, and compared to the composition in corresponding maternal feces. Anaerobes outnumbered facultative anaerobes in all seven neonates within the first days of life, owing to high levels of Bifidobacterium and unexpectedly also Bacteroides, which were inversely correlated. Four neonates harbored maternal levels of Bacteroides, comprising typical adult species throughout the neonatal period, while in three neonates this population was detected at subdominant levels only. In contrast, the major adult-type butyrate-producing anaerobic populations, Roseburia and Faecalibacterium, remained undetectable during the neonatal period. The presence of Bacteroidetes as pioneer bacteria in the majority of neonates studied shows for the first time that adult-type strict anaerobes may reach adult-like population densities within the first week of life, and consequently that the switch from facultative to strict anaerobes may occur earlier than previously assumed in breast-fed neonates. Furthermore, the major adult-type butyrate-producers have never been extensively studied in neonates and the fact that other strict anaerobes are able to establish early suggest that their establishment is rather limited to the absence of metabolic cross-feeding between members of the microbiota than to the absence of anaerobic conditions.