{"doi":"10.1101/2021.06.04.447087","title":"Targeted High-Resolution Taxonomic Identification of <i>Bifidobacterium longum</i> subsp. <i>infantis</i> Using Human Milk Oligosaccharide Metabolizing Genes","abstract":"Abstract Bifidobacterium longum subsp. infantis ( B. infantis ) 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 B. infantis from its close relatives, B. longum and B. suis . All three organisms are classified in the same species group but only B. infantis can metabolize human milk oligosaccharides (HMOs). We compared HMO-metabolizing genes across different Bifidobacterium genomes and developed B. infantis -specific primers to determine if the genes alone or the primers can be used to quickly characterize B. infantis . We showed that B. infantis 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 B. infantis -specific primers. We observed that only 15 of 203 (7.4%) children under 2 years old from a cohort of US children harbored B. infantis . These results highlight the importance of developing and improving approaches to identify B. infantis . A more accurate characterization may provide insights into regional differences of B. infantis prevalence in infant gut microbiota.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2021,"id":216765,"datarank":0.3002025527244853,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.058786865859370235,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.058786865859370235,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":3,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9599,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":625326,"name":"Kevin S. Bonham","orcid":"0000-0003-3200-7533","position":1,"is_corresponding":false},{"id":730493,"name":"Alyssa Fishbein","orcid":null,"position":2,"is_corresponding":false},{"id":626776,"name":"Sophie Rowland","orcid":null,"position":3,"is_corresponding":false},{"id":625327,"name":"Vanja Klepac‐Ceraj","orcid":"0000-0001-5387-5706","position":4,"is_corresponding":false},{"id":56601,"name":"Lauren Tso","orcid":null,"position":0,"is_corresponding":true}],"reference_count":71,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-18T23:53:15.868165Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}