Dynamics of the infant microbiomes onset: exploring the gut and the oral microbiota in full-term and pre-term infants in the frame of mother’s milk microbial ecosystem

The gut microbiota assembly during the very first days of life plays a pivotal role in the education of the immune system and in the building of a healthy status later in life. Besides the mode of delivery, also the feeding type and the gestational age have an impact on the gut microbiota composition. For this reason, by means of next-generation sequencing of the 16S rRNA gene on Illumina MiSeq, we characterized and compared the intestinal bacterial community in 2 cohorts of infants, 1 constituted by 36 healthy breast-fed infants born full-term and the other constituted by 21 infants born moderate to late pre-term (32 to 37 weeks) receiving different types of feeding (mother breast milk, human breast milk from donor and formula). The first cohort was sampled at 20th day of life, whilst the second one was sampled longitudinally from birth to 30th day of life. In addition, also the infant’s saliva and the mother’s milk were sampled and sequenced. The characterization of the 3 ecosystems in full-term infants led to the hypothesis that the mother milk, together with the microorganisms that reside in the baby’s mouth, may act as seeding community and may participate to infant gut microbiota assembly. On the other hand, in the moderately-to late pre-term cohort, the extreme diversity of the infant’s clinical history provokes a tremendous inter-individual variability. Nevertheless, milk and saliva microbiological structures resembled the ones of full-term cohort. The gut microbiota instead presented a very different composition and it is plausible that its establishment is strongly influenced by the infant’s clinical history and environmental bacteria than the mutual relationship with the mother.