Distinct early gut microbiota patterns by delivery mode within 100 hours of birth

doi:10.5409/wjcp.v15.i2.117841

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Jun 9, 2026 (publication date) through May 16, 2026

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World Journal of Clinical Pediatrics

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2219-2808

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Baishideng Publishing Group Inc, 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA

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Copyright: ©Author(s) 2026. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution-NonCommercial (CC BY-NC 4.0) license. No commercial re-use. See permissions. Published by Baishideng Publishing Group Inc.

World J Clin Pediatr. Jun 9, 2026; 15(2): 117841
Published online Jun 9, 2026. doi: 10.5409/wjcp.v15.i2.117841

Distinct early gut microbiota patterns by delivery mode within 100 hours of birth

Palittiya Sintusek, Pavit Klomkliew, Suthida Visedthorn, Kittima Phutthawong, Tanawan Noicharoen, Areewan Soontornsook, Duc Long Tran, Sunchai Payungporn

Palittiya Sintusek, Duc Long Tran, Center 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

Pavit Klomkliew, Suthida Visedthorn, Kittima Phutthawong, Sunchai Payungporn, Center of Excellence in Systems Microbiology, Department of Biochemistry, Chulalongkorn University, Bangkok 10330, Thailand

Tanawan Noicharoen, Areewan Soontornsook, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand

Duc Long Tran, Faculty of Medicine, Can Tho University of Medicine and Pharmacy, Can Tho 90000, Vietnam

Author contributions: Sintusek P conceptualized and designed the study, designed the data collection instruments, collected data, carried out the initial analyses, drafted the initial manuscript, and critically reviewed the manuscript; Payungporn S conceptualized the study, designed and contributed to the experiments, confirmed the validity of the data, and critically reviewed and revised the manuscript; Klomkliew P, Visedthorn S, and Phutthawong K conducted the experiments, analyzed the data, interpreted the results, and reviewed the manuscripts; Noicharoen T, Soontornsook A, and Tran DL designed, collected the data, and reviewed the manuscript; all authors approved the final manuscript as submitted and agreed to be accountable for all aspects of the work.

Supported by Ratchadapiseksompotch Funds, Graduate Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand, No. RA67/040; and Thailand Science research and Innovation Fund Chulalongkorn University, No. HEA_FF_69_225_3000_031.

Institutional review board statement: This study was approved by the Institutional Review Board of the Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (No. 0855/66).

Clinical trial registration statement: The clinical trial is registered on clinicalTrials.gov (NCT06309199, first posted date 13/03/2024).

Informed consent statement: Written informed consent was obtained from all participating neonates' parents or legal guardians. All procedures were conducted in accordance with the Declaration of Helsinki and local ethical standards.

Conflict-of-interest statement: All authors have completed and submitted the International Committee of Medical Journal Editors Uniform Disclosure Form for Potential Conflicts of Interest. None of the authors discloses any conflict of interest.

CONSORT 2010 statement: The authors have read the CONSORT 2010 statement, and the manuscript was prepared and revised according to the CONSORT 2010 statement.

Data sharing statement: The data, analytic methods, and study materials from this study will be made available to other researchers upon reasonable request to the corresponding author. Sequencing data have been deposited in Sequence Read Archive under accession number PRJNA1265435, and metadata will be shared in de-identified form to protect participant confidentiality. To request access to the data, please contact Suthida Visedthorn (tangsuthida.chula@gmail.com). A temporary access link will be generated upon request; note that the link will expire shortly after its creation.

Corresponding author: Palittiya Sintusek, MD, PhD, Associate Professor, Center of Excellence in Thai Pediatric Gastroenterology, Hepatology and Immunology, Division of Gastroenterology, Department of Pediatrics, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV, Pathumwan, Bangkok 10330, Thailand. palittiya.s@chula.ac.th

Received: December 17, 2025
Revised: January 19, 2026
Accepted: February 24, 2026
Published online: June 9, 2026
Processing time: 147 Days and 15.9 Hours

Abstract

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.

Keywords: Gut microbiota; Neonate; Early life; Feeding; Normal labor; Cesarean section

Core Tip: This study characterizes the gut microbiota of healthy neonates within the first 100 hours after birth, which is a critical yet understudied window of microbial establishment. Neonates delivered by vaginal delivery showed early enrichment of Bifidobacterium, whereas those delivered by cesarean delivery exhibited a higher abundance of skin and environment-associated taxa and reduced colonization by Bifidobacterium despite predominant breastfeeding. These findings highlight the role of delivery mode as a key determinant of early microbial assembly and the need for targeted microbiota-supportive strategies for cesarean-born neonates.