Tracing the early bacterial settlers in preterm and very-low birth-weight infants: first report of microbiota dynamics in South American neonates

Mortality in very-low birth-weight (VLBW) infants accounts for up to 50%-70% of the neonatal mortality and up to 25%-30% of infant mortality. Despite the global increase in survival rates, this population remains at heightened risk for developing long-term neurodevelopmental delays, chronic lung disease, malnutrition, and visual and hearing disabilities. The gut microbial composition of VLBW differs from full-term infants and is typically dominated by pathobionts. In this study, we characterized the bacterial composition of the VLBW infant microbiota born at Pereira Rossell Children's Hospital (academic, tertiary referral center) in Montevideo, Uruguay by sequencing the full-length 16S rRNA gene using Oxford Nanopore Technologies. We describe a high predominance of <i>Klebsiella pneumoniae</i> and <i>Escherichia coli</i> in these infants. By sequencing stool samples from two time points, we show that the microbial community diversity increases over time with a higher relative abundance of <i>Bacteroides</i> and <i>Veillonella</i>. Moreover, we describe the effect on the microbial composition of long antibiotic exposure. Different species of the <i>Klebsiella</i> genus, along with <i>Escherichia coli, Enterobacter cloacae</i>, <i>Citrobacter freundii,</i> and <i>Veillonella parvula</i> were observed at a higher relative abundance in patients with more than 5 days of antibiotic treatment. Taken together, our findings shed light on the development and establishment of microbial communities in early-life microbial communities in South America. Our results point to postnatal antibiotics as a major factor orchestrating this process. The integration of microbial community health considerations into preterm clinical care is crucial for improving long-term infant development.