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Updated: Sep 21, 2025
A Method for Targeted 16S Sequencing of Human Milk Samples
Published on: March 23, 2018
Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted
Stephanie B Orchanian1, Julia M Gauglitz1,2,3, Stephen Wandro1
1Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA.
Insights
Infant antibiotic exposure significantly delays gut microbiome development and body site differentiation in preterm infants. The skin microbiome remains resilient, while gut metabolomes mature, with specific bile acid changes observed in non-antibiotic treated infants.
Area of Science:
- Microbiology
- Neonatal Research
- Metabolomics
Background:
- The first week of life is crucial for infant microbiome establishment.
- Preterm infants experience unique challenges impacting their microbiome, including C-section, antibiotics, and NICU environments.
Purpose of the Study:
- To profile the daily development of gut, skin, and oral microbiomes in preterm infants during the first week post-birth.
- To investigate the impact of early life factors, particularly antibiotic exposure, on infant microbiome development.
Main Methods:
- Paired metabolomics and 16S rRNA sequencing data were collected daily for the first week.
- Microbiome development was analyzed across gut, skin, and oral sites.
- Metabolomic profiles were compared between different infant groups.
Main Results:
- The skin microbiome showed resilience to early life perturbations.
- Direct infant antibiotic exposure, not maternal transmission, delayed microbiome development and body site differentiation.
- Gut metabolomes of preterm infants trended towards full-term profiles.
- Primary bile acid metabolism increased significantly only in non-antibiotic treated, vaginally birthed preterm infants.
Conclusions:
- Infant antibiotic exposure is a primary driver of delayed microbiome development in high-risk preterm populations.
- The study provides a framework for multi-omic analyses in preterm infants.
- Identifies potential monitoring and intervention points related to infant antibiotic use.
Abstract:
The first week after birth is a critical time for the establishment of microbial communities for infants. Preterm infants face unique environmental impacts on their newly acquired microbiomes, including increased incidence of cesarean section delivery and exposure to antibiotics as well as delayed enteral feeding and reduced human interaction during their intensive care unit stay. Using contextualized paired metabolomics and 16S sequencing data, the development of the gut, skin, and oral microbiomes of infants is profiled daily for the first week after birth, and it is found that the skin microbiome appears robust to early life perturbation, while direct exposure of infants to antibiotics, rather than presumed maternal transmission, delays microbiome development and prevents the early differentiation based on body site regardless of delivery mode. Metabolomic analyses identify the development of all gut metabolomes of preterm infants toward full-term infant profiles, but a significant increase of primary bile acid metabolism only in the non-antibiotic treated vaginally birthed late preterm infants. This study provides a framework for future multi-omic, multibody site analyses on these high-risk preterm infant populations and suggests opportunities for monitoring and intervention, with infant antibiotic exposure as the primary driver of delays in microbiome development.
