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Background  The gut microbiome has an important role in infant health and immune development and may be affected by early-life exposures. Maternal diet may influence the infant gut microbiome through vertical transfer of maternal microbes to infants during vaginal delivery and breastfeeding. We aimed to examine the association of maternal diet during pregnancy with the infant gut microbiome 6 weeks post-delivery in mother-infant dyads enrolled in the New Hampshire Birth Cohort Study. Infant stool samples were collected from 145 infants, and maternal prenatal diet was assessed using a food frequency questionnaire. We used targeted sequencing of the 16S rRNA V4-V5 hypervariable region to characterize infant gut microbiota. To account for differences in baseline and trajectories of infant gut microbial profiles, we stratified analyses by delivery mode.    Results  We identified three infant gut microbiome clusters, characterized by increased abundance of  Bifidobacterium ,  Streptococcus  and  Clostridium , and  Bacteroides , respectively, overall and in the vaginally delivered infant stratum. In the analyses stratified to infants born vaginally and adjusted for other potential confounders, maternal fruit intake was associated with infant gut microbial community structure (PERMANOVA,  p  < 0.05). In multinomial logistic regression analyses, increased fruit intake was associated with an increased odds of belonging to the high  Streptococcus / Clostridium  group among infants born vaginally (OR (95% CI) = 2.73 (1.36, 5.46)). In infants delivered by Cesarean section, we identified three clusters that differed slightly from vaginally delivered infants, which were characterized by a high abundance of  Bifidobacterium , high  Clostridium  and low  Streptococcus  and  Ruminococcus  genera, and high abundance of the family  Enterobacteriaceae . Maternal dairy intake was associated with an increased odds of infants belonging to the high  Clostridium  cluster in infants born by Cesarean section (OR (95% CI) = 2.36 (1.05, 5.30)). Linear models suggested additional associations between maternal diet and infant intestinal microbes in both delivery mode strata.    Conclusions  Our data indicate that maternal diet influences the infant gut microbiome and that these effects differ by delivery mode.    Electronic supplementary material  The online version of this article (10.1186/s40168-018-0490-8) contains supplementary material, which is available to authorized users.

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner