Background: In preterm infants the intestinal microbiome differs markedly from term infants. However, it is unclear whether the microbiome follows infant specific maturation patterns or whether it is mainly characterized by varying states of dysbiosis. We investigated the development of the intestinal microbiome in extremely preterm infants over time by 16S rRNA amplicon sequencing. We analysed the first meconium and faecal samples from the 2 nd , 3 rd and 4 th weeks, and (clinical) metadata to identify the main factors influencing the microbiota composition development. Results: The study included 41 extremely preterm infants (gestational age 25-30 weeks; birth weight (BW) 430-990g). Birth via Caesarean section (CS) was associated with placental insufficiency during pregnancy and lower BW. In meconium and in weeks 2 and 3 an increased combined abundance of Escherichia and Bacteroides (maternal aerotolerant fecal bacteria) was associated with vaginal delivery (p=0.039, p=0.0002, p=0.034, respectively) while Staphylococcus epidermidis (skin bacterium) was associated with CS (p=0.001, p=0.0003 p=0.048, respectively). Secondly, a switch was observed from a microbiome dominated by S. epidermidis (Bacilli) towards a microbiome dominated by Enterobacteriaceae (Gammaproteobacteria, mainly represented by Klebsiella and Escherichia ), in which the stage of progression appeared to be dependent upon the current weight of the infant, irrespective of the week of sampling or the mode of birth. Conclusions: Our data shows that the mode of delivery does affect the meconium microbiome composition. It also suggests that the weight of the infant at the time of sampling is a better predictor for the stage of progression of the intestinal microbiome development/maturation than gestational/postnatal age. We hypothesize that impaired growth, for example due the effects of diminished placental function during pregnancy, is a key factor in the maturation of the intestinal microbiome in extreme premature infants.
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