Related Experiment Video
Updated: Jun 2, 2026

Applying Advanced In Vitro Culturing Technology to Study the Human Gut Microbiota
Published on: February 15, 2019
Distinct early gut microbiota patterns by delivery mode within 100 hours of birth
Palittiya Sintusek1, Pavit Klomkliew2, Suthida Visedthorn2
1Center of Excellence in Thai Pediatric Gastroenterology, Hepatology and Immunology, Division of Gastroenterology, Department of Pediatrics, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand. palittiya.s@chula.ac.th.
Insights
Cesarean section (CS) delivery in neonates is linked to altered gut microbiota composition and reduced beneficial Bifidobacterium colonization within the first 100 hours. Targeted strategies may support CS-infant gut health.
Area of Science:
- Microbiology
- Neonatal Health
- Gut Microbiome Research
Background:
- Early-life gut microbiome disruptions are linked to health issues.
- Limited research exists on gut microbiota establishment in the immediate postnatal period.
Purpose of the Study:
- To characterize the gut microbiota of neonates within the first 100 hours after birth.
- To investigate the impact of delivery mode on early microbial colonization.
Main Methods:
- Analysis of stool samples from 140 healthy neonates using 16S rDNA sequencing.
- Categorization of samples by delivery mode (vaginal delivery vs. cesarean section) and collection time.
- Assessment of microbiota diversity and composition.
Main Results:
- Cesarean section (CS) delivery was associated with higher gut microbiota diversity (alpha and beta).
- A reduction in gut microbiota diversity was observed 48 hours post-birth.
- CS neonates showed reduced Bifidobacterium colonization and increased skin/environmental taxa compared to vaginal delivery infants.
Conclusions:
- Delivery mode significantly influences early gut microbial assembly in neonates.
- CS-delivered infants exhibit distinct gut microbiota profiles, with reduced beneficial bacteria.
- Targeted interventions are needed to promote healthy gut microbiota in infants born via CS.
Background:
Disruptions in the early-life gut microbiome have been reported to be associated with various health conditions. However, few studies have investigated the establishment of the gut microbiota in the immediate postnatal period.
Aim:
To characterize the gut microbiota of neonates within the first 100 hours after birth.
Methods:
A total of 512 healthy neonates born at a tertiary hospital were enrolled in this study. Stool samples were collected between March 2024 and December 2024 and categorized by delivery mode and stool collection time. Microbiota diversity and composition were assessed using full-length 16S rDNA sequencing. Stool samples from 140 neonates with predominant breastfeeding were analyzed.
Results:
Of the 140 neonates, 70 (50%) were female, 66 (47.1%) were delivered by vaginal delivery (VD), 74 (52.9%) were delivered by cesarean section (CS), and 87 (62.1%) were firstborn. The time of stool collection ranged from 13.2 minutes to 109.82 hours. A significant difference in the time of stool collection was observed between CS and VD neonates (43.0 hours; 95%CI: 35.8-50.1 vs 32.4 hours; 95%CI: 27.8-36.9; P = 0.016). Gut microbiota analysis revealed that CS was associated with higher alpha diversity (Chao1 and Shannon indices; P < 0.001) and beta diversity (P < 0.001). A reduction in the gut microbiota diversity was observed 48 hours after birth (P < 0.001). Escherichia coli predominated in the VD samples. Bifidobacterium species, including Bifidobacterium longum, Bifidobacterium pseudocatenulatum, and Bifidobacterium bifidum, emerged significantly 48 hours after birth. CS neonates exhibited a higher relative abundance of skin- and environmental-associated taxa, including Staphylococcus, Streptococcus, and Pseudomonas, and markedly reduced colonization by Bifidobacterium species despite predominant breastfeeding.
Conclusion:
Despite predominant breastfeeding, CS neonates showed reduced colonization by Bifidobacterium and a greater abundance of skin- and environment-associated taxa within the first 100 hours of life. These findings indicate that delivery mode can be a key determinant of early microbial assembly and highlight the need for targeted strategies to support the establishment of beneficial microbiota in CS-delivered infants.
Related Concept Videos
Development of Human Microbiota
Development of the Oral Microbiota
Anatomy of the Intestines
Small Intestines
The small intestine is an ~7 meter-long tube with an inner diameter of just 2.5 cm. Since most nutrients are absorbed here, the inner lining of the small...
Introduction to the Human Microbiota
Microbiota Modulation by Antibiotics
Microbiota of the Stomach and Small Intestine

