U.S. Babies Are Missing a Key Gut Microbe, Fueling Allergy Risk (Jun 2025, n=412) Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis Early development 

Michael Harrop

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https://gizmodo.com/study-says-u-s-babies-are-missing-a-key-gut-microbe-fueling-allergy-risk-2000619622
https://www.nature.com/articles/s42003-025-08274-7

New research suggests the lack of a bacterium known to help infants digest breast milk could have significant consequences for the developing immune system.

The researchers found that 76% of U.S. infant guts had deficient levels of Bifidobacteria, and 25% had no detectable Bifidobacteria. These bacteria play a critical role in infant health and development, particularly when it comes to protecting babies from chronic illness.

From the 412 participants, the researchers received 210 follow-up health surveys at two years of age. Among these babies, 30% had an adverse health outcome, with 12.4% reporting allergies, 21.0% reporting eczema or dermatitis, and 3.3% reporting asthma. Statistical analysis revealed that babies with deficient levels or a total lack of Bifidobacteria—who made up 76% of the participants—were at greater risk of developing chronic immune conditions. What’s more, the researchers found thatinfant Bifidobacterium has a protective effect, reducing relative risk in the population.

Abstract​

The composition of the infant gut microbiome is critical to immune development and noncommunicable disease (NCD) trajectory. However, a comprehensive evaluation of the infant gut microbiome in the United States is lacking.

The My Baby Biome study, designed to address this knowledge gap, evaluated the gut microbiomes of 412 infants (representative of U.S. demographic diversity) using metagenomics and metabolomics. Regardless of birth mode and/or feeding method, widespread Bifidobacterium deficit was observed, with approximately 25% of U.S. infants lacking detectable Bifidobacterium. Bifidobacterium-dominant microbiomes exhibit distinct features when compared to microbiomes with other dominant microbial compositions including reduced antimicrobial resistance and virulence factor genes, altered carbohydrate utilization pathways, and altered metabolic signatures.

In C-section birth infants, Bifidobacterium tended to be replaced in the human milk oligosaccharide utilization niche with potentially pathogenic species. Longitudinal health outcomes from these infants suggest that the disappearance of key Bifidobacterium may contribute to the development of atopy.
 
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