A WIDESPREAD deficit of Bifidobacterium in infants in the USA is driving prevalent gut dysbiosis, irrespective of birth mode or feeding method.
The infant gut microbiome plays a critical role in immune development and the long-term risk of noncommunicable diseases (NCD). Despite its importance, comprehensive data on the microbial composition of the gut in infants in the USA has been limited. The My Baby Biome study sought to address this gap by conducting a large-scale, demographically representative analysis of infant gut microbiota in the United States. This investigation sheds light on emerging microbial patterns that may have significant implications for paediatric health and clinical practice.
Researchers analysed stool samples from 412 infants in the USA using advanced metagenomic and metabolomic profiling. Strikingly, approximately 25% of infants showed no detectable Bifidobacterium, a genus considered foundational to healthy early-life microbiome development. Regardless of whether infants were delivered vaginally or via Caesarean section, and whether they were breastfed or formula-fed, this deficit was consistently observed. Infants whose microbiomes were dominated by Bifidobacterium had notably lower levels of genes associated with antimicrobial resistance and virulence, as well as distinct metabolic and carbohydrate utilisation profiles. In contrast, C-section infants frequently exhibited colonisation by potentially pathogenic bacteria occupying the niche typically held by Bifidobacterium, particularly for human milk oligosaccharide utilisation. Preliminary longitudinal data from the cohort indicates that infants lacking Bifidobacterium may have an increased risk of developing atopic conditions, underscoring the immunological importance of this genus.
These findings highlight a concerning shift in early-life microbial colonisation patterns in the United States, with potential downstream impacts on child health. From a clinical perspective, the consistent Bifidobacterium deficit raises important questions about perinatal interventions and early feeding strategies. Restoration of this key genus, through targeted probiotic supplementation or maternal microbiota support, could represent a valuable avenue for reducing the risk of atopic and other immune-related conditions. Future research should focus on causal mechanisms linking microbial disruptions with disease trajectories, and on developing clinical guidelines to support microbiome-friendly practices in neonatal care.
Reference
Jarman JB et al. Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis. Commun Biol. 2025 Jun 24;8(1):867.
