Human milk oligosaccharides are distinctly processed by early life gut microbial sialidases

The infant gut microbiome in early life is shaped by numerous factors, including feeding method. Exclusively breastfed and formula-fed infants exhibit distinct microbiome compositions. While these effects are well-established, the underlying mechanisms that drive these differences are not fully understood. Here, we examine the removal of sialic acid from human milk oligosaccharides (HMOs) influenced by human microbial sialidases in early life. We identify 351 and 214 unique sialidase sequences from adult and infant microbiome metagenomes, respectively, and characterize a diverse, representative set in vitro using sialylated HMOs normally present in human breastmilk. We find these proteins exhibit distinct abilities to metabolize 3'- and 6'-sialyllactose, which are the most abundant sialylated HMOs in breastmilk, and distinctly process other more complex substrates, as well. We provide structural insights into these functional differences by pinpointing active site features uniquely present in efficient enzymes and show that these results extend to activities on complex mixtures of sialylated HMOs purified from human breastmilk. Finally, we demonstrate in human clinical data that distinct profiles of sialidase-encoding bacterial taxa are observed in breastfed and formula-fed infants at 1 and 4 months of age, prior to the introduction of solid foods. Together, these findings show that specific bacterial sialidases are influential in shaping the early gut microbiome, data that may improve the supplementation of infant formulas for enhanced developmental outcomes.