Targeted High-Resolution Taxonomic Identification of subsp. Using Human Milk Oligosaccharide Metabolizing Genes.

subsp. () is one of a few microorganisms capable of metabolizing human breast milk and is a pioneer colonizer in the guts of breastfed infants. One current challenge is differentiating from its close relatives, and . All three organisms are classified in the same species group but only can metabolize human milk oligosaccharides (HMOs). We compared HMO-metabolizing genes across different genomes and developed -specific primers to determine if the genes alone or the primers can be used to quickly characterize . We showed that is uniquely identified by the presence of five HMO-metabolizing gene clusters, tested for its prevalence in infant gut metagenomes, and validated the results using the -specific primers. We observed that only 15 of 203 (7.4%) children under 2 years old from a cohort of US children harbored . These results highlight the importance of developing and improving approaches to identify . A more accurate characterization may provide insights into regional differences of prevalence in infant gut microbiota.