Chronicling the development of the salivary and gastrointestinal microbiome in very preterm neonates

Introduction Establishment of the gastrointestinal microbiome is known to play a defining role in both the short- and long-term health of preterm infants. Following birth, microbial colonization of the gut progresses from the oropharynx to anus, making saliva a unique biofluid that may provide insight into aberrant microbial colonization in real-time. The objective of this pilot, observational study was to compare saliva and stool microbial profiles serially collected in the first two weeks of life in very preterm newborns (< 32 weeks' gestation) to determine the colonization patterns in saliva and stool. Methods Six stool and saliva samples were obtained concurrently within the first two weeks of life in very preterm infants. 16s rRNA V1-V3 sequencing was performed. Alpha and beta diversity of stool and saliva microbiome were analyzed based upon sex, mode of delivery, antibiotic exposure, presence of a central line, level of respiratory support and other morbidities. Results Twenty preterm newborns (gestational ages: 27–32 weeks; birth weight: 730–2,090 grams) participated in this pilot study. Saliva and stool samples collected (total n = 210) at the first time-point had the highest microbial diversity. Male neonates, newborns born via vaginal delivery, newborns with central lines, and newborns exposed to both maternal and neonatal antibiotics had the highest alpha diversity. Overall, neonates without antibiotic exposure had lower alpha diversity in both stool and saliva samples compared to subjects with any antibiotic exposure. Staphylococcus was the dominant genus in both stool and saliva, however, beta diversity between saliva and stool were dissimilar (Adonis R 2 = 0.062, and Anosim R = 0.1953, p < 0.05). Discussion In this pilot study, maternal and neonatal antibiotic exposure, sex, mode of delivery and presence of central line alter the neonatal microbiome. Salivary microbial profiling does not appear to be predictive of stool microbial profiles in the first two weeks of life. Future studies are warranted to further explore the establishment of aberrant microbiomes in preterm infants.