Background: Interactions between the neonate host and its gut microbiome are central to the development of a healthy immune system. However, the mechanisms by which animals alter early colonization of microbiota for their benefit remain unclear. Host-derived carbohydrates, which can serve as metabolic substrates for the expansion of specific commensal and pathogenic bacteria, are one method by which the host may influence interspecies competition in the microbiome. Here, we investigated the role of early-life expression of the α2,6-sialyltransferase ST6GAL1 in microbiome phylogeny and mucosal immunity. Methods: Intestinal sialylation was characterized by RT-qPCR, immunoblot, microscopy, and sialyltransferase enzyme assays in genetic mouse models at rest or with glucocorticoid receptor modulators. The fecal, upper respiratory, and oral microbiomes of pups expressing or lacking St6gal1 were analyzed by 16S rRNA sequencing. Pooled fecal microbiomes from syngeneic donors were transferred to antibiotic-treated wild-type mice, before analysis of recipient mucosal immune responses by flow cytometry, RT-qPCR, microscopy, and ELISA. Results: ST6GAL1 was highly expressed in duodenal enterocytes between birth and weaning, driving temporary sialylation of the associated glycocalyx and secretion of active ST6GAL1 into the intestinal lumen, with subsequent uptake by colonic goblet cells. Expression was mediated by the P1 promoter of the St6gal1 gene, which was efficiently inhibited by intraperitoneal dexamethasone. At weaning, the fecal microbiome of St6gal1-KO pups was unchanged in diversity but exhibited reductions in Clostridium, Coprobacillus, and Adlercreutzia, along with increased Helicobacter and Bilophila. Transfer of St6gal1-KO microbiome induced an AhR-dependent Th17 response, with expression of T-bet and IL-17, and IL-22-dependent gut lengthening. Conclusions: Intestinal sialylation by the sialyltransferase ST6GAL1 in the neonatal period is a developmentally regulated host mechanism coordinating bacterial colonization in the early gut microbiome. The inability to produce α2,6-sialyl ligands results in microbiome-dependent Th17 inflammation, highlighting a pathway by which intestinal epithelium regulates mucosal immunity. Considering the prevalence of intestinal fucosylation in adult animals, sialic acid may promote an early stage of ecological succession in the developing gut. Trial registration: N/A