Identification of a novel Human Milk Oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei

Abstract The infant gut microbiome is impacted by early-life feeding, as human milk oligosaccharides (HMOs) found in breastmilk, cannot be digested by infants, and serve as nutrients for their gut bacteria. While the vast majority of HMO-utilization research has focused on Bifidobacterium species, recent studies have suggested additional HMO-utilizers, mostly Bacteroides, yet their utilization mechanism is completely unknown. Here, we investigated Bacteroides dorei isolates from breastfed-infants and identified that polysaccharide utilization locus (PUL) 32 enables B. dorei to utilize sialylated HMOs. We performed transcriptional profiling and identified upregulated genes when growing on sialylated HMOs. Using CRISPR-Cas12 to knock-out four PUL32 genes, with combined complementation assays, we identified GH33 as the critical gene in PUL32 for sialylated HMO-utilization. This is the first demonstration of an HMO-utilization system by a Bacteroides species isolated from infants, opening the way to further characterization of additional such systems, to better understand HMO-utilization in the infant gut.