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Noninvasive molecular fingerprinting of host-microbiome interactions in neonates

Sharon M Donovan1, Mei Wang1, Marcia H Monaco1

  • 1Department of Food Science and Human Nutrition, University of Illinois, Urbana, IL 61801, USA.

FEBS Letters
|July 22, 2014
PubMed

Insights

Researchers developed a new method to study infant gut development using exfoliated intestinal cells. This approach reveals differences in gene expression and microbiome interactions between breast-fed and formula-fed infants, aiding in understanding gut health.

Area of Science:

  • Developmental Biology
  • Microbiology
  • Immunology
  • Gastroenterology

Background:

  • The early postnatal period is crucial for intestinal and immune system maturation.
  • Diet (breast milk vs. formula) significantly impacts infant gut microbiome composition and development.
  • Studying host-microbe interactions in infant intestines is ethically challenging due to the need for biopsies.

Purpose of the Study:

  • To develop a non-invasive analytical framework for examining host and microbial responses in the infant gut.
  • To investigate differences in gene expression and microbiome interactions between breast-fed and formula-fed infants.
  • To compare host responses in exfoliated intestinal cells between preterm and term infants.

Main Methods:

  • Development of a statistically rigorous analytical framework using exfoliated intestinal epithelial cells.
  • Simultaneous analysis of host gene expression (transcriptome) and microbiome composition.
  • Differential gene expression analysis and canonical correlation analysis to link host and microbial factors.
  • Comparison of exfoliated cells from preterm and term infants.

Main Results:

  • Significant differential gene expression (approx. 1200 genes) related to intestinal proliferation, differentiation, and barrier function was observed between breast-fed and formula-fed infants.
  • A correlation was identified between microbiome virulence genes and host immunity and defense genes.
  • Preterm infants showed up-regulated pathways for immune cell function and inflammation, while term infants exhibited up-regulated cell growth-related genes.

Conclusions:

  • Coordinate measurement of exfoliated epithelial cell transcriptomes and the microbiome provides a novel approach to study infant gut development and host-microbe interactions non-invasively.
  • This method can be used for prospective studies of gut development or retrospective analysis of disease triggers in banked samples.
  • Findings highlight diet-specific host responses and differing maturation pathways in preterm versus term infants.

Keywords:
Exfoliated cellGene expressionInfantIntestineMicrobiomeNutrition

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