Probiotic Supplementation Impacts Gut Microbiota Development in Infants at Risk of Atopy: A Follow-Up Analysis of a Randomised, Double-Blind, Placebo-Controlled Study

Early-life gut microbiota establishment plays a role in lifelong health, with disruptions linked to heightened risks of metabolic and immune disorders. Probiotic supplementation may be used to modulate the infant gut microbiome to promote favourable development and here we evaluate how Lab4B probiotic supplementation shapes infant gut microbiota development over the first six months. Faecal samples collected from infants enrolled in the PROBAT (ISRCTN26287422) randomised, double-blind, placebo-controlled trial were analysed using culture-dependent, and independent (16S rDNA and metagenomic shotgun sequencing) techniques to examine the composition, diversity, antimicrobial resistance gene (ARG) abundance, and metabolic capabilities of the microbiotas. Probiotic supplementation encouraged the development of a distinct microbiota composition: characterised by elevated abundances of Bifidobacteriaceae in the first 6 weeks (p = 0.006) and Lactobacillaceae throughout the first 6 months (p < 0.05 at every 6-week time point), accelerated microbial diversification, reduced abundance of beta-lactam and cephalosporin resistance genes and differences in predicted metabolic capabilities at start and end points. Supplementation of this high atopy risk neonatal population with the Lab4B probiotic significantly influenced the development of the infant gut microbiota during the first 6 months.