Antibiotics and the developing intestinal microbiome, metabolome and inflammatory environment in a randomized trial of preterm infants

Sci Rep. 2021 Jan 21;11(1):1943. doi: 10.1038/s41598-021-80982-6.


Antibiotic use in neonates can have detrimental effects on the developing gut microbiome, increasing the risk of morbidity. A majority of preterm neonates receive antibiotics after birth without clear evidence to guide this practice. Here microbiome, metabolomic, and immune marker results from the routine early antibiotic use in symptomatic preterm Neonates (REASON) study are presented. The REASON study is the first trial to randomize symptomatic preterm neonates to receive or not receive antibiotics in the first 48 h after birth. Using 16S rRNA sequencing of stool samples collected longitudinally for 91 neonates, the effect of such antibiotic use on microbiome diversity is assessed. The results illustrate that type of nutrition shapes the early infant gut microbiome. By integrating data for the gut microbiome, stool metabolites, stool immune markers, and inferred metabolic pathways, an association was discovered between Veillonella and the neurotransmitter gamma-aminobutyric acid (GABA). These results suggest early antibiotic use may impact the gut-brain axis with the potential for consequences in early life development, a finding that needs to be validated in a larger cohort.Trial Registration This project is registered at under the name "Antibiotic 'Dysbiosis' in Preterm Infants" with trial number NCT02784821.

Publication types

  • Randomized Controlled Trial
  • Research Support, N.I.H., Extramural

MeSH terms

  • Anti-Bacterial Agents / administration & dosage*
  • Dysbiosis / drug therapy*
  • Dysbiosis / genetics
  • Dysbiosis / microbiology
  • Dysbiosis / pathology
  • Feces / microbiology
  • Female
  • Gastrointestinal Microbiome / drug effects
  • Humans
  • Infant, Premature
  • Inflammation / drug therapy*
  • Inflammation / genetics
  • Inflammation / microbiology
  • Inflammation / pathology
  • Metabolic Networks and Pathways / genetics
  • Metabolome / drug effects
  • Metabolome / genetics*
  • Metabolomics / methods
  • Microbiota / genetics
  • Pregnancy
  • RNA, Ribosomal, 16S / genetics*
  • Veillonella / genetics
  • Veillonella / metabolism
  • gamma-Aminobutyric Acid / metabolism


  • Anti-Bacterial Agents
  • RNA, Ribosomal, 16S
  • gamma-Aminobutyric Acid

Associated data