Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

•Gut microbiomes of 98 mothers and their infants during the first year of life was assessed•Cessation of breast-feeding drives the maturation of the infant gut microbiome•Shifts in signature species demonstrate nonrandom transitions in the infants’ gut•Changes in nutrient and xenobiotic metabolism mark maturation of the gut microbiome

SummaryThe gut microbiota is central to human health, but its establishment in early life has not been quantitatively and functionally examined. Applying metagenomic analysis on fecal samples from a large cohort of Swedish infants and their mothers, we characterized the gut microbiome during the first year of life and assessed the impact of mode of delivery and feeding on its establishment. In contrast to vaginally delivered infants, the gut microbiota of infants delivered by C-section showed significantly less resemblance to their mothers. Nutrition had a major impact on early microbiota composition and function, with cessation of breast-feeding, rather than introduction of solid food, being required for maturation into an adult-like microbiota. Microbiota composition and ecological network had distinctive features at each sampled stage, in accordance with functional maturation of the microbiome. Our findings establish a framework for understanding the interplay between the gut microbiome and the human body in early life.

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