The gene, which is not active in some mothers, produces a breast milk sugar called "secretors".
Mothers known as "non-secretors" have a non-functional fucosyltransferase 2 (FUT2) gene, which alters the composition of their breast milk sugars and changes how the microbial community, or microbiota, of their infants' guts develop, the study said.
"In no way is the nonsecretor mother's milk less healthy, and their babies are at no greater risk," said senior study author David Mills from the University of California, Davis.
"What this work does show us is that the mother's genotype matters, and that it influences the breast milk, which clearly drives the establishment of microbes in the intestines of their babies," Mills said.
The research may have applications in a clinical setting for protecting premature infants from a range of intestinal diseases including necrotising enterocolitis (NEC), a condition that is the second most common cause of death among premature infants in the US.
The research examined the differences in infant gut microbial populations arising from differences in human milk sugars.
The research was conducted using milk samples from 44 mothers.
The study appeared in the journal Microbiome.
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