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Growing up on a farm is associated with an asthma-protective effect, but the mechanisms underlying this effect are largely unknown. In the Protection against Allergy: Study in Rural Environments (PASTURE) birth cohort, we modeled maturation using 16S rRNA sequence data of the human gut microbiome in infants from 2 to 12 months of age. The estimated microbiome age (EMA) in 12-month-old infants was associated with previous farm exposure (
β
= 0.27 (0.12–0.43),
P
= 0.001,
n
= 618) and reduced risk of asthma at school age (odds ratio (OR) = 0.72 (0.56–0.93),
P
= 0.011). EMA mediated the protective farm effect by 19%. In a nested case–control sample (
n
= 138), we found inverse associations of asthma with the measured level of fecal butyrate (OR = 0.28 (0.09–0.91),
P
= 0.034), bacterial taxa that predict butyrate production (OR = 0.38 (0.17–0.84),
P
= 0.017) and the relative abundance of the gene encoding butyryl–coenzyme A (CoA):acetate–CoA-transferase, a major enzyme in butyrate metabolism (OR = 0.43 (0.19–0.97),
P
= 0.042). The gut microbiome may contribute to asthma protection through metabolites, supporting the concept of a gut–lung axis in humans.
Growing up in the rich microbial environment of a farm strongly influences the maturation of the gut microbiome in the first year of life, which helps protect against the development of asthma in children.