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Updated: Dec 29, 2025
Probiotic Studies in Neonatal Mice Using Gavage
Published on: January 27, 2019
Neonatal microbiota development and the effect of early life antibiotics are determined by two distinct settler types
Anat Eck1, Nicole B M M Rutten2, Maartje M J Singendonk3
1Department of Medical Microbiology and Infection Control, Amsterdam UMC, VU University Amsterdam, Amsterdam, The Netherlands.
Insights
Antibiotic exposure in newborns significantly impacts gut microbiota development, particularly Bacteroidetes diversity and colonization, with effects lasting up to three months. Understanding infant gut microbiome dynamics is crucial for long-term health.
Area of Science:
- Microbiology
- Neonatal Health
- Gastroenterology
Background:
- The neonatal period is critical for establishing the infant gut microbiota.
- Antibiotic exposure during infancy can disrupt microbiome development and is linked to later-life disorders.
- Early-life gut microbiome composition influences infant health outcomes.
Purpose of the Study:
- To investigate intestinal microbiota development in term infants during the first three months of life.
- To assess the impact of antibiotic exposure in the first week of life on infant gut microbiota.
- To identify distinct infant gut microbiota profiles ('settler types') and their relationship with delivery mode.
Main Methods:
- Fecal samples collected from 98 infants at one week, one month, and three months post-birth.
- Microbial composition analyzed using IS-pro, comparing antibiotic-treated and untreated infants.
- Analysis stratified by feeding type and delivery mode, with a focused analysis on vaginally-born, exclusively breastfed infants.
Main Results:
- Infant gut microbiota at one week clustered into two 'settler types' based on Bacteroidetes abundance, with Caesarean-born infants predominantly in the low-Bacteroidetes group.
- Antibiotic administration led to reduced Bacteroidetes diversity and/or delayed colonization, persisting for three months.
- Antibiotics significantly altered Bacteroidetes composition and dynamics, indicating a differential microbiota development.
Conclusions:
- Early-life antibiotic exposure profoundly affects infant gut microbiota composition and development, particularly Bacteroidetes.
- The identified 'settler types' may represent distinct microbial colonization patterns influenced by delivery mode.
- Stratifying infant cohorts by 'settler types' could uncover subtle group effects in microbiome research.
Abstract:
The neonatal period, during which the initial gut microbiota is acquired, is a critical phase. The healthy development of the infant's microbiome can be interrupted by external perturbations, like antibiotics, which are associated with profound effects on the gut microbiome and various disorders later in life. The aim of this study was to investigate the development of intestinal microbiota and the effect of antibiotic exposure during the first three months of life in term infants. Fecal samples were collected from healthy infants and infants who received antibiotics in the first week of life at one week, one month, and three months after birth. Microbial composition was analyzed using IS-pro and compared between antibiotics-treated and untreated infants. In total, 98 infants, divided into four groups based on feeding type and delivery mode, were analyzed. At one week of age, samples clustered into two distinct groups, which were termed "settler types", based on their Bacteroidetes abundance. Caesarean-born infants belonged to the low-Bacteroidetes settler type, but vaginally-born infants were divided between the two groups. The antibiotics effect was assessed within a subgroup of 45 infants, vaginally-born and exclusively breastfed, to minimize the effect of other confounders. Antibiotics administration resulted in lower Bacteroidetes diversity and/or a delay in Bacteroidetes colonization, which persisted for three months, and in a differential development of the microbiota. Antibiotics resulted in pronounced effects on the Bacteroidetes composition and dynamics. Finally, we hypothesize that stratification of children's cohorts based on settler types may reveal group effects that might otherwise be masked.
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