EARLY differences in newborn gut microbiota composition may influence the risk of hospitalisation for viral lower respiratory tract infections (vLRTIs) in early childhood, according to findings from a UK birth cohort study.
The Baby Biome Study (BBS), a prospective cohort enrolling mother–infant pairs from three UK hospitals between 2016–2017, investigated whether stool microbiota profiles from the first week of life were associated with vLRTI outcomes in the first 2 years. Stool samples were analysed using shotgun metagenomic sequencing to assess microbial diversity and community structure. Hospital admission data were obtained via linkage with the Hospital Episode Statistics-Admitted Patient Care (HES-APC) database, and associations were evaluated using Poisson mixed-effects models adjusted for key confounders.
Out of 3,476 enrolled infants, 1.082 met all inclusion criteria with available microbiota sequencing and follow-up data. Most were born at term (92% ≥37 weeks) and without comorbidities (97%). The study found that higher gut microbiota alpha diversity in the first week of life was associated with a significantly reduced risk of vLRTI hospitalisation: Chao1 Index adjusted hazard ratio [aHR]: 0.92 (95% CI: 0.85–0.99), Shannon Index aHR: 0.57 (0.33–0.98), and Simpson Index aHR: 0.36 (0.11–1.20). Additionally, three microbiota clusters were identified. Cluster 3, dominated by Bifidobacterium longum and seen only in vaginally delivered babies, was associated with the lowest vLRTI risk. In contrast, clusters with a mixed composition (Cluster 1) or dominated by Bifidobacterium breve (Cluster 2) were linked to significantly higher risks of vLRTI hospitalisation (HR: 3.05 [1.25–7.41] and 2.80 [1.06–7.44], respectively).
These findings suggest that early gut microbial profiles, particularly species composition and diversity, may influence vulnerability to respiratory infections. The results point to specific bacterial species as potential targets for future preventive interventions in infancy.
Reference
Garcia-Mauriño C et al. Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics. Lancet Microbe. 2025; DOI: 10.1016/j.lanmic.2024.101072.
