Biology subjects

Shmorak, S.

Publications and source records attributed to Shmorak, S..

2 recordsLinked to original sources

bioRxiv2025

Development of the preterm infant gut and gastric residuals microbiome

Prematurity, defined as birth before 37 completed weeks of gestation, is the leading cause of mortality in children under five and affects approximately 11% of live births globally--around 15 million infants each year. Despite advances in neonatal care, preterm infants remain at an increased risk for a range of complications. One widely used clinical practice in neonatal intensive care units (NICUs) is the monitoring of gastric residuals (GRs) to assess feeding tolerance and guide enteral nutrition. While the clinical significance of GRs is debated, their microbial composition has not been extensively studied. In this study, we performed metagenomic sequencing of 199 stool and 69 GR samples from 39 preterm infants during hospitalization to characterize their gut and stomach microbiomes. To our knowledge, this is the first study to describe the microbial landscape of GR in preterm infants. We identified 11 distinct GR clusters, often dominated by Staphylococcus, Streptococcus, and Klebsiella, with microbial diversity correlating with GR aspiration frequency. Longitudinal analysis revealed temporal colonization patterns, with early dominance of Staphylococcus epidermidis and Bradyrhizobium, and later emergence of Escherichia coli, Staphylococcus hominis, and Streptococcus thermophilus. In stool samples, 8 microbial clusters were found, frequently enriched with Enterobacteriaceae. Early samples rich in S. epidermidis were associated with higher gestational age and lower microbial richness, while Bifidobacterium breve, a beneficial gut commensal, appeared later in hospitalization. Comparative analysis showed overlap between gut and gastric microbiota, though stomach samples were more dynamic and exhibited less intra-subject similarity. Strain-level resolution revealed both subject-specific (e.g., E. coli, K. pneumoniae) and widely shared (e.g., S. epidermidis) taxa. We also identified a pathogenic Klebsiella aerogenes strain associated with bacteremia with distinct genomic features a week ahead of its first clinical isolation. These findings provide novel insights into the dynamic and niche-specific microbial colonization of preterm infants.

microbiology↗

bioRxiv2023

Longitudinal Variability of Bifidobacterium Species in the Infant Gut is Independent of Maternal Milk HMO Composition

The development of the infant gut microbiome is primarily influenced by the infant feeding type, with breast milk serving as the optimal source of nutrition. Breast milk contains human milk oligosaccharides (HMOs) that act as nourishment for the developing gut microbiome, potentially conferring advantages to specific bacterial species. Previous studies have demonstrated the ability of certain Bifidobacterium species to utilize individual HMOs, however a longitudinal study examining the evolving microbial community at a high resolution in the context of mothers milk HMO composition is lacking. Here, we explored the relationship between the HMO composition in mothers milk and the abundance of Bifidobacterium species in the infant gut throughout the course of early life. To enable subspecies taxonomic classification, we developed a high-throughput method for quantifying the abundance of Bifidobacterium longum subsp. infantis (BL. infantis; the best known HMO-utilizer) from metagenomic sequencing. We applied this method to a longitudinal cohort consisting of 21 mother-infant dyads, from whom we collected matched breast milk and infant stool samples at multiple time points during the first year of life. We observed substantial changes in the infant gut microbiome over the course of several months, while the HMO composition in mothers milk remained relatively stable. Bifidobacterium species were a prominent factor contributing to the variation observed among samples; however, no significant associations were found between specific HMOs in mothers milk and the abundance of Bifidobacterium species. Finally, the longitudinal nature of our cohort enabled us to characterize the dynamic colonization of BL. infantis in the infant gut, which surprisingly began late in the breastfeeding period. Applying our BL. infantis quantification method to additional datasets from various geographical locations, we found similar, late-colonization by BL. infantis, highlighting the importance of quantifying BL. infantis in the infant gut.

microbiology↗