The development of the preterm infant gut and gastric residual microbiome

The infant gut microbiome assembly begins soon after birth and maintains a pivotal role in infant development and health status. Preterm birth is the leading cause of mortality among children. In Israel, preterm infants in the neonatal intensive care unit undergo extractions of gastric residuals following feeding. There has been a lack of research addressing the concurrent development of gastric residuals and gut microbiome in preterm infants despite the clinical insights that could be gained.

To address these challenges we enrolled 40 preterm infants in Hadassah Medical Center, to study the early life development of the preterm infant gut and gastric residuals microbiome. We collected stool and gastric residual samples, supplemented with clinically relevant hospitalization data. Our high sampling frequency and longitudinal study design enable us to observe and understand the trajectory of the early-life gut microbiome and explore personalized microbiome aspects such as sharing of bacterial strains across inter- and intra-subject samples.

We have conducted, to the best of our knowledge, the first metagenomic gastric residuals microbial analysis detecting bacterial species and strains shared in the infant’s gut and stomach. Additionally, we have observed personalized colonization patterns of the gut microbiome and found species such as Escherichia coli, and Enterococcus faecalis showing high subject-specific dominant strain stability, suggestive of a personalized dominant strain. In contrast, Staphylococcus epidermidis dominant strains are shared across subjects consistent with environmental colonization.

Finally, our work provides an opportunity to explore the early life development of the preterm infant gut and the gastric residual microbiome.