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RestoreGut - restoration of the gut microbiome after birth by caesarean section: study protocol for a double-blinded, randomised, placebo-controlled trial

Year: 2026

Type: article

Abstract: Introduction Birth by caesarean section (CS) is associated with early gut microbiome perturbations and an increased risk of childhood asthma, likely reflecting long-term immune imprinting. This trial aims to restore the gut microbiota in CS-born infants through faecal microbiota transplantation (FMT) and faecal virome transplantation (FVT). Methods and analysis RestoreGut is a double-blinded, randomised, placebo-controlled trial enrolling 60 elective CS-born and 20 vaginally born infants. CS-born infants are randomised to receive maternal FMT, FVT or placebo in the first hours after birth. FMTs and FVTs are derived from pathogen-screened maternal stool samples collected during late pregnancy, using a novel bacterial enumeration technique to standardise dosing. Infant stool samples are collected on days 1, 3 and 7, and at 1, 3, 6 and 12 months after birth and analysed for microbiome composition over time using metagenomic sequencing. The primary outcome is differences in microbiome composition between the treatment and placebo groups at the 1-week timepoint. Secondary outcomes include longitudinal differences in gut microbiome and virome composition across all subsequent timepoints during the first year of life, differences in infection incidence during the first year of life, differences in faecal metabolomic profiles and comparisons of infant microbiomes in the FMT, FVT and placebo groups to those of a vaginally born reference cohort. Ethics and dissemination This trial has received approval from the Committees on Health Research Ethics in the Capital Region of Denmark (Approval ID H-24002284). The results will be disseminated through peer-reviewed publications and the trial website, targeting both scientific audiences and the general public. Trial registration number NCT06264219.

Source: BMJ Open

DOI: 10.1136/bmjopen-2026-126018