{"doi":"10.1101/2024.07.06.602360","title":"Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria","abstract":"Bifidobacteria are among the earliest colonizers of the human gut and are widely used as probiotics for their health-promoting properties. However, individual responses to probiotic supplementation may vary with strain type(s), microbiota composition, diet, or lifestyle conditions, highlighting the need for strain-level insights into the bifidobacterial metabolism of dietary and host glycans. Here, we systematically reconstructed 68 pathways involved in the utilization of mono-, di-, oligo-, and polysaccharides by analyzing the distribution of 589 curated metabolic functional roles (catabolic enzymes, transporters, transcriptional regulators) in 3083 non-redundant cultured Bifidobacterium isolates and metagenome-assembled genomes (MAGs) of human origin. Our analysis uncovered extensive inter- and intraspecies heterogeneity, including a distinct clade within the Bifidobacterium longum species capable of metabolizing α-glucans. We also identified isolates of Bangladeshi origin that harbor unique gene clusters implicated in the breakdown of xyloglucan and human milk oligosaccharides. Thirty-eight predicted carbohydrate utilization phenotypes were experimentally validated in 30 geographically diverse Bifidobacterium isolates in vitro. Our large-scale genomic compendium expands the knowledge of bifidobacterial carbohydrate metabolism and can inform the rational design of probiotic and synbiotic formulations tailored to strain-specific nutrient preferences.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":487167,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9465,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":314949,"name":"Dmitry A. Rodionov","orcid":"0000-0002-0939-390X","position":1,"is_corresponding":false},{"id":1331532,"name":"Matthew Charles Hibberd","orcid":null,"position":2,"is_corresponding":false},{"id":316130,"name":"Janaki L. Guruge","orcid":null,"position":3,"is_corresponding":false},{"id":1331533,"name":"James D Kent","orcid":null,"position":4,"is_corresponding":false},{"id":103983,"name":"Marat D. Kazanov","orcid":"0000-0002-2314-5507","position":5,"is_corresponding":false},{"id":314950,"name":"Semen A. Leyn","orcid":"0000-0002-9886-9120","position":6,"is_corresponding":false},{"id":1331534,"name":"Marinela L Elane","orcid":null,"position":7,"is_corresponding":false},{"id":1129497,"name":"Kristija Sejane","orcid":"0009-0004-9643-0458","position":8,"is_corresponding":false},{"id":1331535,"name":"Annalee Furst","orcid":null,"position":9,"is_corresponding":false},{"id":240567,"name":"Lars Bode","orcid":"0000-0002-9914-9571","position":10,"is_corresponding":false},{"id":314951,"name":"Michael J. Barratt","orcid":"0000-0003-3794-1296","position":11,"is_corresponding":false},{"id":19791,"name":"Jeffrey I. Gordon","orcid":"0000-0001-8304-3548","position":12,"is_corresponding":false},{"id":42087,"name":"Andrei L. Osterman","orcid":"0000-0002-3810-9824","position":13,"is_corresponding":false},{"id":872758,"name":"Aleksandr A. Arzamasov","orcid":"0000-0002-4150-4817","position":0,"is_corresponding":true}],"reference_count":126,"raw_metadata":null,"created_at":"2026-07-19T02:08:06.013846Z","pmid":"39005317","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":[]}