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Summary Mode of delivery strongly influences the early infant gut microbiome. Children born by cesarean section (C-section) lack Bacteroides species until 6–18 months of age. One hypothesis is that these differences stem from lack of exposure to the maternal vaginal microbiome. Here, we re-evaluate this hypothesis by comparing the microbial profiles of 75 infants born vaginally or by planned versus emergent C-section. Multiple children born by C-section have a high abundance of Bacteroides in their first few days of life, but at 2 weeks, both C-section groups lack Bacteroides (primarily according to 16S sequencing), despite their difference in exposure to the birth canal. Finally, a comparison of microbial strain profiles between infants and maternal vaginal or rectal samples finds evidence for mother-to-child transmission of rectal rather than vaginal strains. These results suggest differences in colonization stability as an important factor in infant gut microbiome composition rather than birth canal exposure., Graphical Abstract, Highlights Week 1 gut microbiota does not differ between infants born vaginally versus C-section Week 2 gut microbiota of C-section infants lacks Bacteroides Microbiota of infants born by C-section after labor resembles scheduled C-section Bacterial strains in infants match maternal rectal rather than vaginal strains, Mitchell et al. compare early-life infant gut microbiota by delivery mode, suggesting early colonization by Bacteroides regardless of delivery mode, but loss of Bacteroides by 2 weeks in C-section-delivered infants, whether or not exposed to the vagina in labor. Infant strains matched maternal rectal rather vaginal strains.