The Role of the Neonatal Gut Microbiota in the Encephalopathy of Prematurity: A Comprehensive Study

Academic Background

Premature birth (defined as birth before 37 weeks of gestation) is a common issue globally, affecting approximately 10% of pregnancies. Preterm infants are at risk of abnormal brain development, known as Encephalopathy of Prematurity (EOP), which can lead to cerebral palsy, neurodevelopmental disorders, autism, and psychiatric conditions. Currently, there are no effective treatments for EOP, partly because the mechanisms linking premature birth to abnormal brain development are not fully understood.

The second and third trimesters of pregnancy are critical periods for brain development. Premature birth and its associated exposures and morbidities can cause injury and dysmaturation in the developing brain, leading to regional brain growth abnormalities, diffuse white matter lesions, abnormal cortical and deep gray matter (DGM) development, and structural connectivity issues. These features of EOP are visible on structural and diffusion magnetic resonance imaging (MRI) during the neonatal period and are associated with subsequent neurocognitive development, making them intermediate phenotypes for investigating the upstream determinants of brain development.

The acquisition and progression of the gut microbiota coincide with fundamental neurodevelopmental processes in early life. Preclinical and human observational studies suggest that the gut microbiome modulates neural functions through the microbiota-gut-brain axis. Specifically, the rapid parallel development of the brain and gut microbiota in early life has led to the hypothesis of “nested sensitive periods,” where brain development interacts with gut microbiota development to shape cognition and behavior. This hypothesis is supported by a growing body of literature reporting associations between gut microbiota features and cognitive, language, motor, and socio-emotional development in childhood.

Preterm infants may be particularly vulnerable to disruptions in the microbiota-gut-brain axis due to altered microbiota development, which can arise from the early exposure of the immature gastrointestinal tract to microbial colonization. Although the general pattern of microbiota development in the first months of life appears similar in term and preterm infants, preterm infants have lower bacterial diversity and lower abundances of essential microbes like Bifidobacterium, while opportunistic pathogens such as Klebsiella, Enterobacter, Enterococcus, and Staphylococcus are more abundant. This may result from routine exposure to potent modifiers of the pioneering microbiota, including maternal and neonatal antibiotic treatments and variable nutritional exposures during the first months of life in a neonatal intensive care unit (NICU) setting.

Although the preterm population has a high burden of neurocognitive impairment and alterations in the gut microbiota, only a few recent studies have investigated the gut microbiota in direct relation to preterm infant neurodevelopment or overt parenchymal brain injuries. Most of these studies have been small, and the directions of effects vary, but there is some consensus that abundances of Bifidobacteriaceae, Enterococcaceae, Enterobacteriaceae (e.g., Escherichia/Shigella, Enterobacter, and Klebsiella), Clostridium, and Veillonella may correlate with outcomes. Since EOP is the prevailing form of brain dysmaturation after preterm birth, moving beyond assessing overt parenchymal injuries and complex behavioral traits to study designs that include multimodal brain MRI data is crucial to elucidate the understanding of microbiome-brain interactions in this vulnerable population. The gut microbiota is intrinsically modifiable by mode of feeding and enteral supplements; thus, this knowledge could offer potential new avenues for perinatal neuroprotection.

Study Source

This study was conducted by Kadi Vaher, Manuel Blesa Cabez, Paula Lusarreta Parga, and colleagues from the University of Edinburgh, University Medical Center Utrecht, and other institutions. The paper was published on December 17, 2024, in Cell Reports Medicine, titled The Neonatal Gut Microbiota: A Role in the Encephalopathy of Prematurity.

Study Process and Results

Study Process

This study characterized the fecal microbiome in a cohort of 147 neonates enriched for very preterm birth using 16S rRNA gene and shotgun metagenomic sequencing. The data were integrated with term-equivalent structural and diffusion brain MRI to explore associations between the gut microbiome and EOP.

1. Sample Collection and Processing:

   • Fecal samples were collected from preterm infants at birth (TP1: meconium) and prior to discharge from the NICU (TP2: fecal sample), and from term-born controls at birth.
   • Samples were analyzed using 16S rRNA gene sequencing and shotgun metagenomic sequencing.

2. Microbiome Analysis:

   • The intestinal microbiome profiles of preterm and term infants were characterized using 16S rRNA gene sequencing and shotgun metagenomic sequencing.
   • Principal coordinate analysis (PCO) and alpha diversity analysis were used to explore associations between microbiome composition and MRI markers of EOP.

3. Brain MRI Analysis:

   • Preterm infants underwent structural and diffusion brain MRI at term-equivalent age, capturing brain size (tissue volumes), microstructure (e.g., fractional anisotropy [FA], radial diffusivity [RD], neurite density index [NDI], orientation dispersion index [ODI]), and cortical morphometry (e.g., gyrification index, thickness, sulcal depth, curvature, and surface area).

4. Functional Analysis:

   • Gut metabolic modules (GMMs) and gut-brain modules (GBMs) were calculated from the metagenomic data to explore the functional capacity of the gut microbiome and its relationship with brain microstructure.

Key Results

1. Associations Between Microbiome Composition and EOP:

   • The gut microbiota of preterm infants underwent significant changes between birth and discharge, with increased diversity and dominance of Bifidobacterium or Enterobacteriaceae (mainly Klebsiella).
   • The abundances of Escherichia coli and Klebsiella spp. correlated with microstructural parameters in deep and cortical gray matter, particularly with NDI and ODI.
   • The abundance of Veillonella correlated with DGM microstructural parameters and was associated with gestational age at scan.

2. Functional Analysis:

   • Escherichia coli and Klebsiella spp. may interact with brain microstructure via tryptophan and propionate metabolism.
   • Bifidobacterium was positively associated with total brain and white matter volumes, suggesting its potential role in brain growth through metabolic pathways.

Conclusions and Significance

By integrating gut microbiome and multimodal brain MRI data, this study revealed associations between the gut microbiota and EOP in preterm infants. The results suggest that the composition and functional capacity of the gut microbiota are closely related to the development of brain microstructure in preterm infants, particularly through the metabolic activities of Escherichia coli and Klebsiella spp. These findings provide new potential avenues for neuroprotection in preterm infants, suggesting that modulating the gut microbiota may improve neurodevelopmental outcomes.

Study Highlights

1. Key Findings: This study is the first to systematically explore the associations between the gut microbiota and EOP in preterm infants, revealing potential links between specific bacteria (e.g., Escherichia coli and Klebsiella spp.) and brain microstructure.
2. Methodological Innovation: The study combined 16S rRNA gene sequencing and shotgun metagenomic sequencing with multimodal brain MRI data to comprehensively assess brain development.
3. Practical Implications: The results offer new insights into neuroprotection for preterm infants, suggesting that modulating the gut microbiota may improve neurodevelopmental outcomes.

Additional Valuable Information

The limitations of this study include the relatively small sample size, the multidimensional nature of microbiome and brain MRI data, and the complexity of the analyses. Future studies with larger sample sizes are needed to validate these findings and further explore the causal relationships between the gut microbiota and brain development. Additionally, incorporating metabolomics analyses will help to better understand how the gut microbiota influences brain development through metabolic pathways.