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Aberrant microbiota signatures precede symptom development in infantile colic

Emmy Van Daele¹, Kim Kamphorst^2,3, Clara Belzer¹

¹Laboratory of Microbiology, Wageningen University and Research, Wageningen, the Netherlands.

Journal of Pediatric Gastroenterology and Nutrition

|June 9, 2025

Abstract

Objective:

To identify microbial alterations preceding, during, and following infantile colic (IC).

Methods:

In the Dutch prospective INCA (INtestinal microbiota Composition after AB treatment in early life) cohort study, 184 term-born infants were included, of whom 30 had IC. Fecal samples were collected from each infant at eight time points from birth to 2 years and analyzed by 16S rRNA gene amplicon sequencing.

Results:

The feces of infants with IC exhibited a significantly different microbiota composition persisting up to 6 months compared to those without IC, characterized by elevated relative abundance of members of the Pseudomonadota and diminished Actinomycetota. Microbial alterations were more pronounced in early-onset IC (≤4 weeks) than late-onset IC (≥4 weeks). Late-onset IC manifested as an early surge in Bacteroides spp. from the first day of life. Streptococcus spp. increased during the crying periods of approximately 30 and 90 days for early- and late-onset IC, respectively. Antibiotic (AB) exposure in the first week was associated with AB-specific (Days: 2-365) and IC-dependent (Days: 2-30) genera, with an increase in Enterococcus and a decrease in Bifidobacterium spp.

Conclusions:

IC was preceded by a different development of the gut microbiota compared to non-IC infants, and these differences were more pronounced in early-onset IC infants. AB exposure in the first week appeared to have specific and overlapping effects on the infants' gut microbiota. These findings may help develop future prevention and treatment approaches for IC.

Trial Registration:

ClinicalTrials.gov identifier: NCT02536560.

Keywords:

excessive crying gastrointestinal health intestinal microbiota

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