Gut Microbiota Development in Preterm Infants

Colonisation of the gastrointestinal tract commences at birth and proceeds through a well-defined succession of microbial communities. In preterm infants, immaturity of gut physiology, broad-spectrum antibiotic use and prolonged stays in neonatal intensive care units disrupt this trajectory. Early colonisers are typically facultative anaerobes such as Staphylococcus and Enterococcus, followed by Enterobacteriaceae, before obligate anaerobes including Bifidobacterium emerge. Delay or failure in this shift can result in a persistently low-diversity ecosystem, heightening the risk of necrotising enterocolitis and late-onset sepsis. Human milk, with its complex oligosaccharides, supports growth of beneficial bacteria and production of short-chain fatty acids, which in turn reinforce epithelial integrity and modulate immune development. Probiotic interventions have been introduced to accelerate establishment of commensal taxa and to reduce reservoirs of antibiotic resistance. A nuanced understanding of microbial succession and functional capacity in preterm cohorts underpins efforts to devise feeding regimens, antimicrobial stewardship and targeted biotherapeutics that collectively aim to shape a resilient microbial ecosystem and improve long-term health trajectories.

Research from Nature Portfolio

Recent studies have demonstrated that preventive regimens combining specific probiotic strains with human milk feeding exert profound effects on microbiome maturation. Supplementation with Bifidobacterium longum subsp. infantis alongside human milk oligosaccharides not only accelerates the transition to an anaerobe-dominated community but also markedly reduces carriage of antibiotic resistance genes compared with alternative probiotic or no supplementation protocols. Furthermore, longitudinal analyses in very low birthweight infants reveal that gestational age is the principal driver of microbial succession. Four distinct phases characterised respectively by dominance of Staphylococcus, Enterococcus, Enterobacter and Bifidobacterium have been delineated. Extremely premature infants experience a prolonged Enterococcus phase, delaying the final maturation step towards bifidobacterial colonisation. Antibiotic exposure imposes transient perturbations, while mode of delivery exerts minimal long-term influence.

Gut Microbiota Development in Preterm Infants publication trend

The graph below shows the total number of articles in gut microbiota development in preterm infants across all publications each year (not limited to Nature Index journals).

Technical terms

Gut microbiota: The community of bacteria, archaea, fungi and viruses inhabiting the gastrointestinal tract.

Dysbiosis: A departure from a healthy microbial balance, often marked by reduced diversity or overrepresentation of pathogenic taxa.

Shotgun metagenomics: Unbiased sequencing of all genetic material in a sample to profile microbial composition and functional potential.

Human milk oligosaccharides (HMOs): Complex carbohydrates in breast milk that selectively nourish beneficial gut bacteria.

Short-chain fatty acids (SCFAs): Metabolic by-products of microbial fermentation that support gut epithelial health and immune regulation.

References

1. Clinical NEC prevention practices drive different microbiome profiles and functional responses in the preterm intestine. Nature Communications (2023).
2. Clinical sequelae of gut microbiome development and disruption in hospitalized preterm infants. Cell Host & Microbe (2024).
3. Intestinal microbiota development and gestational age in preterm neonates. Scientific Reports (2018).